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/7787258/working' mkdir: created directory `/scratch/stefan/7787258/working/protonate' Storing results in /scratch/stefan/7787258/finished Working in /scratch/stefan/7787258/working /scratch/stefan/7787258/working /scratch/stefan/7787258 /scratch/stefan/7787258/working/protonate /scratch/stefan/7787258/working /scratch/stefan/7787258 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1070 protomers created Coalesing and merging protomers 1037 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1057 protomers after new stereo-center expansion /scratch/stefan/7787258/working /scratch/stefan/7787258 Bulk generating 3D conformations all protomers in /scratch/stefan/7787258/working/3D mkdir: created directory `/scratch/stefan/7787258/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7787258/working/protonate/xaaabrt-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' 1058 3D conformations generated for 1000 compounds Building REAL300025478150 mkdir: created directory `/scratch/stefan/7787258/working/building' mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478150' /scratch/stefan/7787258/working/building/REAL300025478150 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478150 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478150/0 /scratch/stefan/7787258/working/building/REAL300025478150 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1 `/scratch/stefan/7787258/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@@H]1C(F)F) `REAL300025478150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478150 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@@H]1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 65, 65, 65, 65, 65, 1, 14, 25, 25, 29, 29, 29, 29, 29, 34, 34, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 14, 65, 1, 1, 29, 29, 34] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45]) 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: REAL300025478150 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@@H]1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 19, 29, 29, 29, 29, 42, 42, 86, 116, 201, 201, 201, 201, 201, 29, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 19, 19, 29, 29, 29, 29, 29, 86, 86, 201, 29, 29, 1, 1, 5] 201 rigid atoms, others: [43, 44, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478150 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@@H]1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 138, 65, 65, 65, 65, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 65, 181, 198, 198, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 138, 138, 65, 65, 65, 65, 65, 37, 37, 1, 65, 65, 201, 201, 201] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478150 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478150 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `/scratch/stefan/7787258/finished' Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478150/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478150 Building REAL300025478151 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478151' /scratch/stefan/7787258/working/building/REAL300025478151 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478151 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478151/0 /scratch/stefan/7787258/working/building/REAL300025478151 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/2 `/scratch/stefan/7787258/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)N1) `REAL300025478151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 16, 55, 55, 55, 55, 55, 1, 13, 28, 28, 56, 56, 56, 56, 56, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 55, 1, 1, 56, 56] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 231 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: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 20, 40, 56, 56, 56, 56, 72, 72, 119, 144, 201, 201, 201, 201, 201, 56, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 40, 40, 56, 56, 56, 56, 56, 119, 119, 201, 56, 56, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 641 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: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 105, 55, 55, 55, 55, 50, 42, 50, 13, 1, 1, 1, 1, 1, 1, 1, 55, 118, 160, 160, 201, 201, 201, 201, 201, 118, 118, 118, 105, 105, 55, 55, 55, 55, 55, 42, 42, 1, 55, 55, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 688 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478151 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478151/1 /scratch/stefan/7787258/working/building/REAL300025478151 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/3 `/scratch/stefan/7787258/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)[N-]1) `REAL300025478151.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 69, 69, 69, 69, 69, 1, 19, 38, 38, 39, 39, 39, 39, 39, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 13, 13, 69, 1, 1, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 25, 39, 39, 39, 39, 49, 49, 95, 123, 201, 201, 201, 201, 201, 39, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 39, 39, 39, 39, 39, 95, 95, 201, 39, 39, 1] 201 rigid atoms, others: [41, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478151 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 124, 69, 69, 69, 69, 47, 41, 47, 13, 1, 1, 1, 1, 1, 1, 1, 69, 163, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 124, 124, 69, 69, 69, 69, 69, 41, 41, 1, 69, 69, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478151 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478151 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478151/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478151/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478151 Building REAL300025478152 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478152' /scratch/stefan/7787258/working/building/REAL300025478152 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478152 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478152/0 /scratch/stefan/7787258/working/building/REAL300025478152 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/4 `/scratch/stefan/7787258/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478152 none CC=CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 21, 11, 21, 10, 11, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 73, 73, 73, 73, 73, 1, 35, 35, 35, 35, 35, 21, 63, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 73, 1, 1] 603 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 319 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478152 none CC=CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 197, 143, 197, 142, 143, 132, 142, 73, 73, 73, 73, 51, 41, 51, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 197, 591, 142, 142, 142, 132, 132, 73, 73, 73, 73, 73, 41, 41, 1, 73, 73] 603 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 1458 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478152 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478152 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478152/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478152 Building REAL300025478153 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478153' /scratch/stefan/7787258/working/building/REAL300025478153 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478153 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478153/0 /scratch/stefan/7787258/working/building/REAL300025478153 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/5 `/scratch/stefan/7787258/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478153 none CCCC[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 22, 9, 22, 22, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 55, 55, 55, 55, 55, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 22, 22, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 12, 12, 55, 1, 1] 201 rigid atoms, others: [16, 47, 12, 11, 44, 13, 14, 45, 48, 52, 46, 26, 15, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51]) total number of confs: 244 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: REAL300025478153 none CCCC[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 91, 170, 170, 91, 91, 88, 91, 55, 55, 55, 55, 44, 33, 44, 12, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 91, 91, 91, 88, 88, 55, 55, 55, 55, 55, 33, 33, 1, 55, 55] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 935 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478153 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478153 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478153/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478153 Building REAL300025478154 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478154' /scratch/stefan/7787258/working/building/REAL300025478154 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478154 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478154/0 /scratch/stefan/7787258/working/building/REAL300025478154 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/6 `/scratch/stefan/7787258/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478154 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 6, 7, 16, 16, 16, 16, 16, 1, 6, 7, 7, 7, 6, 6, 6, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 6, 6, 16, 1, 1, 7, 7, 7, 7, 7, 7] 16 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 65 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: REAL300025478154 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 16, 11, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 1, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 40 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478154 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478154/1 /scratch/stefan/7787258/working/building/REAL300025478154 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/7 `/scratch/stefan/7787258/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C) `REAL300025478154.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478154 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 19, 40, 15, 19, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 73, 73, 73, 73, 73, 1, 40, 47, 47, 40, 40, 40, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 14, 14, 73, 1, 1, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 316 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: REAL300025478154 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 179, 186, 155, 179, 73, 73, 73, 73, 49, 38, 49, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 179, 179, 179, 155, 155, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 807 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478154 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478154 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478154/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478154/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478154 Building REAL300025478155 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478155' /scratch/stefan/7787258/working/building/REAL300025478155 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478155 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478155/0 /scratch/stefan/7787258/working/building/REAL300025478155 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/8 `/scratch/stefan/7787258/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478155 none CCC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 27, 27, 11, 27, 10, 11, 5, 10, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 60, 60, 60, 60, 60, 1, 47, 47, 47, 47, 47, 27, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 9, 9, 60, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478155 none CCC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 131, 117, 131, 117, 117, 106, 117, 60, 60, 60, 60, 43, 31, 43, 12, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 131, 117, 117, 117, 106, 106, 60, 60, 60, 60, 60, 31, 31, 1, 60, 60] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 922 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478155 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478155 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478155/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478155 Building REAL300025478156 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478156' /scratch/stefan/7787258/working/building/REAL300025478156 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478156 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478156/0 /scratch/stefan/7787258/working/building/REAL300025478156 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/9 `/scratch/stefan/7787258/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2(CC2)C12CC2) `REAL300025478156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478156 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2(CC2)C12CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 54, 54, 54, 54, 54, 1, 15, 25, 25, 36, 36, 36, 36, 36, 36, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 13, 13, 54, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 224 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: REAL300025478156 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2(CC2)C12CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 23, 36, 36, 36, 36, 57, 57, 98, 127, 201, 201, 201, 201, 201, 36, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 36, 36, 36, 36, 36, 98, 98, 201, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 556 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: REAL300025478156 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2(CC2)C12CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 112, 54, 54, 54, 54, 41, 32, 41, 12, 1, 1, 1, 1, 1, 1, 1, 54, 136, 154, 154, 201, 201, 201, 201, 201, 201, 136, 136, 136, 112, 112, 54, 54, 54, 54, 54, 32, 32, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478156 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478156 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478156/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478156 Building REAL300025478157 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478157' /scratch/stefan/7787258/working/building/REAL300025478157 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478157 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478157/0 /scratch/stefan/7787258/working/building/REAL300025478157 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/10 `/scratch/stefan/7787258/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478157 none CCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 25, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 70, 70, 70, 70, 70, 1, 40, 40, 40, 40, 40, 25, 25, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 70, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478157 none CCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 122, 122, 122, 114, 122, 70, 70, 70, 70, 54, 41, 54, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 141, 141, 122, 122, 122, 114, 114, 70, 70, 70, 70, 70, 41, 41, 1, 70, 70] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 895 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478157 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478157 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478157/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478157 Building REAL300025478158 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478158' /scratch/stefan/7787258/working/building/REAL300025478158 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478158 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478158/0 /scratch/stefan/7787258/working/building/REAL300025478158 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/11 `/scratch/stefan/7787258/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478158 none CCC(F)(F)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 32, 39, 39, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 58, 58, 58, 58, 58, 1, 39, 39, 39, 39, 39, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478158 none CCC(F)(F)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 201, 119, 119, 119, 107, 119, 58, 58, 58, 58, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 195, 195, 119, 119, 119, 107, 107, 58, 58, 58, 58, 58, 35, 35, 1, 58, 58] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 877 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478158 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478158 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478158/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478158 Building REAL300025478159 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478159' /scratch/stefan/7787258/working/building/REAL300025478159 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478159 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478159/0 /scratch/stefan/7787258/working/building/REAL300025478159 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/12 `/scratch/stefan/7787258/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478159 none CC1=NOC=C1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 37, 46, 46, 46, 46, 54, 54, 106, 126, 201, 201, 201, 201, 201, 46, 2, 2, 2, 1, 7, 7, 17, 17, 17, 37, 37, 46, 46, 46, 46, 46, 106, 106, 201, 46, 46] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478159 none CC1=NOC=C1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 74, 74, 74, 63, 74, 42, 42, 42, 42, 41, 33, 41, 13, 1, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 167, 167, 74, 74, 74, 63, 63, 42, 42, 42, 42, 42, 33, 33, 1, 42, 42] 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, 46, 47]) total number of confs: 782 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478159 none CC1=NOC=C1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 27, 9, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 4, 4, 9, 12, 42, 42, 42, 42, 42, 1, 46, 46, 46, 46, 27, 27, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 9, 9, 42, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 46, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478159 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478159 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478159/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478159 Building REAL300025478160 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478160' /scratch/stefan/7787258/working/building/REAL300025478160 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478160 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478160/0 /scratch/stefan/7787258/working/building/REAL300025478160 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/13 `/scratch/stefan/7787258/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=N1) `REAL300025478160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478160 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 58, 58, 58, 58, 58, 1, 13, 21, 21, 33, 37, 37, 37, 37, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 58, 1, 1, 33, 33, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 242 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478160 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 18, 28, 37, 37, 37, 37, 55, 55, 96, 122, 201, 201, 201, 201, 201, 37, 3, 11, 1, 1, 1, 1, 1, 1, 18, 18, 18, 28, 28, 37, 37, 37, 37, 37, 96, 96, 201, 37, 37, 3, 3, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478160 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 119, 58, 58, 58, 58, 45, 37, 45, 13, 1, 1, 1, 1, 1, 1, 1, 58, 144, 174, 174, 183, 201, 201, 201, 201, 144, 144, 144, 119, 119, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58, 183, 183, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 760 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478160 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478160 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478160/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478160 Building REAL300025478161 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478161' /scratch/stefan/7787258/working/building/REAL300025478161 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478161 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478161/0 /scratch/stefan/7787258/working/building/REAL300025478161 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/14 `/scratch/stefan/7787258/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NC(=O)NN2)C1)C(=O)CN=[N+]=[N-]) `REAL300025478161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478161 none CN(CC1CCN(C(=O)CSC2=NC(=O)NN2)C1)C(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 1, 11, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 2, 2, 14, 23, 31, 31, 31, 31, 31, 1, 9, 15, 15, 26, 45, 45, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 14, 14, 31, 31, 1, 1, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 17, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 40, 41]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478161 none CN(CC1CCN(C(=O)CSC2=NC(=O)NN2)C1)C(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 1, 11, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 60, 31, 31, 31, 31, 21, 15, 21, 12, 1, 1, 1, 1, 1, 1, 1, 31, 77, 86, 86, 136, 201, 201, 77, 77, 77, 60, 60, 31, 31, 31, 31, 31, 15, 15, 1, 1, 31, 31, 136, 136] 201 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478161 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478161/1 /scratch/stefan/7787258/working/building/REAL300025478161 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/15 `/scratch/stefan/7787258/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NC(=O)[N-]N2)C1)C(=O)CN=[N+]=[N-]) `REAL300025478161.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478161 none CN(CC1CCN(C(=O)CSC2=NC(=O)[N-]N2)C1)C(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 1, 11, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 17, 34, 34, 34, 34, 34, 1, 11, 19, 19, 33, 69, 69, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 34, 1, 1, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40]) total number of confs: 261 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478161 none CN(CC1CCN(C(=O)CSC2=NC(=O)[N-]N2)C1)C(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 1, 11, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 7, 3, 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: [94, 77, 34, 34, 34, 34, 28, 25, 28, 8, 1, 1, 1, 1, 1, 1, 1, 34, 94, 115, 115, 150, 201, 201, 94, 94, 94, 77, 77, 34, 34, 34, 34, 34, 25, 25, 1, 34, 34, 150, 150] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 716 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478161 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478161 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478161/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478161/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478161 Building REAL300025478162 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478162' /scratch/stefan/7787258/working/building/REAL300025478162 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478162 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478162/0 /scratch/stefan/7787258/working/building/REAL300025478162 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/16 `/scratch/stefan/7787258/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(=O)N1) `REAL300025478162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478162 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 70, 70, 70, 70, 70, 1, 14, 27, 27, 44, 44, 44, 44, 44, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 15, 15, 70, 1, 1, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 272 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: REAL300025478162 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 33, 44, 44, 44, 44, 58, 58, 101, 128, 201, 201, 201, 201, 201, 44, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 44, 44, 44, 44, 44, 101, 101, 201, 44, 44, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 586 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: REAL300025478162 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 130, 70, 70, 70, 70, 50, 40, 50, 13, 1, 1, 1, 1, 1, 1, 1, 70, 161, 186, 186, 201, 201, 201, 201, 201, 161, 161, 161, 130, 130, 70, 70, 70, 70, 70, 40, 40, 1, 70, 70, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 759 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478162 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478162 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478162/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478162 Building REAL300025478163 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478163' /scratch/stefan/7787258/working/building/REAL300025478163 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478163 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478163/0 /scratch/stefan/7787258/working/building/REAL300025478163 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/17 `/scratch/stefan/7787258/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CO) `REAL300025478163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478163 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 33, 33, 33, 33, 33, 1, 9, 9, 9, 13, 13, 13, 16, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 6, 6, 33, 1, 1, 13, 13, 13, 13, 13, 13, 16, 16, 48] 192 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 192 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478163 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [52, 51, 33, 33, 33, 33, 30, 24, 30, 12, 1, 1, 1, 1, 1, 1, 1, 33, 52, 52, 52, 64, 64, 64, 64, 52, 52, 52, 51, 51, 33, 33, 33, 33, 33, 24, 24, 1, 33, 33, 64, 64, 64, 64, 64, 64, 64, 64, 192] 192 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 470 number of broken/clashed sets: 192 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478163 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478163 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478163/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478163 Building REAL300025478164 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478164' /scratch/stefan/7787258/working/building/REAL300025478164 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478164 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478164/0 /scratch/stefan/7787258/working/building/REAL300025478164 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/18 `/scratch/stefan/7787258/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CN1N=CC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478164 none C=CN1N=CC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 26, 48, 48, 48, 48, 65, 65, 109, 131, 201, 201, 201, 201, 201, 48, 2, 2, 2, 1, 1, 11, 11, 11, 26, 26, 48, 48, 48, 48, 48, 109, 109, 201, 48, 48] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 595 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: REAL300025478164 none C=CN1N=CC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 144, 130, 144, 115, 130, 62, 62, 62, 62, 53, 38, 53, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 130, 130, 130, 115, 115, 62, 62, 62, 62, 62, 38, 38, 1, 62, 62] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 677 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: REAL300025478164 none C=CN1N=CC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 48, 28, 17, 28, 6, 17, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 62, 62, 62, 62, 62, 1, 48, 48, 48, 48, 48, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 12, 12, 62, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478164 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478164 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478164/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478164 Building REAL300025478165 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478165' /scratch/stefan/7787258/working/building/REAL300025478165 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478165 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478165/0 /scratch/stefan/7787258/working/building/REAL300025478165 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/19 `/scratch/stefan/7787258/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1C) `REAL300025478165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478165 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 62, 62, 62, 62, 62, 1, 13, 27, 27, 30, 30, 30, 30, 30, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 62, 1, 1, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478165 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 22, 30, 30, 30, 30, 44, 44, 74, 101, 201, 201, 201, 201, 201, 30, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 30, 30, 30, 30, 30, 74, 74, 201, 30, 30, 1, 1, 2, 2, 2] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478165 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 120, 62, 62, 62, 62, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 62, 158, 199, 199, 201, 201, 201, 201, 201, 158, 158, 158, 120, 120, 62, 62, 62, 62, 62, 39, 39, 1, 62, 62, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478165 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478165 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478165/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478165 Building REAL300025478166 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478166' /scratch/stefan/7787258/working/building/REAL300025478166 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478166 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478166/0 /scratch/stefan/7787258/working/building/REAL300025478166 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/20 `/scratch/stefan/7787258/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C1CC1) `REAL300025478166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478166 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 59, 59, 59, 59, 59, 1, 11, 20, 20, 21, 25, 25, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 59, 1, 1, 21, 21, 25, 75, 32, 32, 32, 32, 32] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478166 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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: [13, 8, 13, 26, 32, 32, 32, 32, 49, 49, 91, 115, 201, 201, 201, 201, 201, 32, 7, 8, 3, 1, 3, 1, 1, 1, 13, 13, 13, 26, 26, 32, 32, 32, 32, 32, 91, 91, 201, 32, 32, 7, 7, 3, 9, 1, 1, 1, 1, 1] 603 rigid atoms, others: [45, 46, 47, 48, 49, 21, 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, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 573 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478166 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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: [156, 124, 59, 59, 59, 59, 41, 32, 41, 11, 1, 1, 1, 1, 1, 1, 1, 59, 156, 190, 190, 192, 192, 192, 201, 201, 156, 156, 156, 124, 124, 59, 59, 59, 59, 59, 32, 32, 1, 59, 59, 192, 192, 192, 576, 201, 201, 201, 201, 201] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478166 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478166 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478166/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478166 Building REAL300025478167 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478167' /scratch/stefan/7787258/working/building/REAL300025478167 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478167 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478167/0 /scratch/stefan/7787258/working/building/REAL300025478167 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/21 `/scratch/stefan/7787258/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478167 none CC(C)CC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 25, 19, 25, 14, 19, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 80, 80, 80, 80, 80, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 25, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 15, 15, 80, 1, 1] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 274 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: REAL300025478167 none CC(C)CC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 195, 201, 189, 195, 167, 189, 80, 80, 80, 80, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 167, 167, 80, 80, 80, 80, 80, 41, 41, 1, 80, 80] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 774 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478167 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478167 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478167/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478167 Building REAL300025478168 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478168' /scratch/stefan/7787258/working/building/REAL300025478168 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478168 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478168/0 /scratch/stefan/7787258/working/building/REAL300025478168 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/22 `/scratch/stefan/7787258/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)COC1) `REAL300025478168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478168 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 45, 45, 45, 45, 45, 1, 15, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478168 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 15, 27, 27, 27, 27, 36, 36, 64, 97, 201, 201, 201, 201, 201, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 27, 27, 27, 27, 27, 64, 64, 201, 27, 27, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478168 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [147, 122, 45, 45, 45, 45, 31, 24, 31, 13, 1, 1, 1, 1, 1, 1, 1, 45, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 122, 122, 45, 45, 45, 45, 45, 24, 24, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478168 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478168 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478168/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478168 Building REAL300025478169 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478169' /scratch/stefan/7787258/working/building/REAL300025478169 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478169 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478169/0 /scratch/stefan/7787258/working/building/REAL300025478169 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/23 `/scratch/stefan/7787258/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478169 none CC(=CC1CC1)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 7, 7, 7, 7, 19, 32, 32, 32, 32, 43, 43, 74, 100, 201, 201, 201, 201, 201, 32, 4, 4, 4, 3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 32, 32, 32, 32, 32, 74, 74, 201, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 34, 30, 31] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 512 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478169 none CC(=CC1CC1)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 149, 149, 201, 201, 99, 100, 91, 99, 54, 54, 54, 54, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 54, 149, 149, 149, 149, 201, 201, 201, 201, 201, 99, 99, 99, 91, 91, 54, 54, 54, 54, 54, 35, 35, 1, 54, 54] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 796 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: REAL300025478169 none CC(=CC1CC1)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 18, 18, 32, 32, 9, 10, 5, 9, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 54, 54, 54, 54, 54, 1, 18, 18, 18, 18, 32, 32, 32, 32, 32, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 9, 9, 54, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478169 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478169 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478169/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478169 Building REAL300025478170 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478170' /scratch/stefan/7787258/working/building/REAL300025478170 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478170 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478170/0 /scratch/stefan/7787258/working/building/REAL300025478170 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/24 `/scratch/stefan/7787258/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=COC=N1) `REAL300025478170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478170 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=COC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 12, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 58, 58, 58, 58, 58, 1, 13, 25, 25, 34, 34, 34, 34, 34, 34, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 206 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: REAL300025478170 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=COC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 12, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 27, 34, 34, 34, 34, 44, 44, 85, 107, 201, 201, 201, 201, 201, 34, 2, 6, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 34, 34, 34, 34, 34, 85, 85, 201, 34, 34, 2, 2, 1, 1] 201 rigid atoms, others: [44, 45, 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]) total number of confs: 553 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: REAL300025478170 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=COC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 12, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 110, 58, 58, 58, 58, 43, 36, 43, 12, 1, 1, 1, 1, 1, 1, 1, 58, 120, 161, 161, 201, 201, 201, 201, 201, 201, 120, 120, 120, 110, 110, 58, 58, 58, 58, 58, 36, 36, 1, 58, 58, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478170 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478170 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478170/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478170 Building REAL300025478171 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478171' /scratch/stefan/7787258/working/building/REAL300025478171 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478171 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478171/0 /scratch/stefan/7787258/working/building/REAL300025478171 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/25 `/scratch/stefan/7787258/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(CO)CCC1) `REAL300025478171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478171 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 19, 56, 56, 56, 56, 56, 1, 12, 21, 21, 25, 36, 37, 36, 36, 36, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 56, 1, 1, 25, 25, 37, 37, 111, 36, 36, 36, 36, 36, 36] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 353 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: REAL300025478171 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 6, 12, 25, 36, 36, 36, 36, 55, 55, 92, 120, 201, 201, 201, 201, 201, 36, 4, 6, 1, 1, 1, 5, 1, 1, 1, 12, 12, 12, 25, 25, 36, 36, 36, 36, 36, 92, 92, 201, 36, 36, 4, 4, 5, 5, 15, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [47, 48, 49, 50, 51, 20, 21, 22, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 611 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: REAL300025478171 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(CO)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [120, 102, 56, 56, 56, 56, 41, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 56, 120, 137, 137, 146, 201, 201, 201, 201, 201, 120, 120, 120, 102, 102, 56, 56, 56, 56, 56, 34, 34, 1, 56, 56, 146, 146, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1396 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478171 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478171 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478171/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478171 Building REAL300025478172 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478172' /scratch/stefan/7787258/working/building/REAL300025478172 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478172 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478172/0 /scratch/stefan/7787258/working/building/REAL300025478172 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/26 `/scratch/stefan/7787258/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=CS1) `REAL300025478172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478172 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 54, 54, 54, 54, 54, 1, 12, 25, 25, 37, 42, 42, 42, 42, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 54, 1, 1, 37, 37, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 253 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: REAL300025478172 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 18, 32, 42, 42, 42, 42, 54, 54, 97, 122, 201, 201, 201, 201, 201, 42, 2, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 32, 32, 42, 42, 42, 42, 42, 97, 97, 201, 42, 42, 2, 2, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 579 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: REAL300025478172 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 54, 54, 54, 54, 41, 32, 41, 13, 1, 1, 1, 1, 1, 1, 1, 54, 123, 161, 161, 179, 201, 201, 201, 201, 123, 123, 123, 106, 106, 54, 54, 54, 54, 54, 32, 32, 1, 54, 54, 179, 179, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 766 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478172 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478172 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478172/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478172 Building REAL300025478173 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478173' /scratch/stefan/7787258/working/building/REAL300025478173 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478173 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478173/0 /scratch/stefan/7787258/working/building/REAL300025478173 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/27 `/scratch/stefan/7787258/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC=CO1) `REAL300025478173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478173 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 72, 72, 72, 72, 72, 1, 15, 31, 31, 33, 33, 33, 33, 33, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478173 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 23, 33, 33, 33, 33, 52, 52, 93, 122, 201, 201, 201, 201, 201, 33, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 33, 33, 33, 33, 33, 93, 93, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478173 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 144, 72, 72, 72, 72, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 72, 184, 201, 201, 201, 201, 201, 201, 201, 184, 184, 184, 144, 144, 72, 72, 72, 72, 72, 42, 42, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478173 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478173 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478173/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478173 Building REAL300025478174 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478174' /scratch/stefan/7787258/working/building/REAL300025478174 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478174 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478174/0 /scratch/stefan/7787258/working/building/REAL300025478174 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/28 `/scratch/stefan/7787258/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CCC1) `REAL300025478174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478174 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 64, 64, 64, 64, 64, 1, 13, 17, 17, 17, 17, 17, 18, 18, 18, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 64, 1, 1, 17, 17, 17, 51, 18, 18, 18, 18, 18, 18, 18] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 574 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478174 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [6, 4, 6, 12, 18, 18, 18, 18, 36, 36, 66, 99, 201, 201, 201, 201, 201, 18, 3, 4, 1, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 18, 18, 18, 18, 18, 66, 66, 201, 18, 18, 3, 3, 3, 9, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [46, 47, 48, 49, 50, 51, 20, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 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: 574 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478174 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [175, 146, 64, 64, 64, 64, 45, 37, 45, 13, 1, 1, 1, 1, 1, 1, 1, 64, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 146, 146, 64, 64, 64, 64, 64, 37, 37, 1, 64, 64, 201, 201, 201, 603, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1365 number of broken/clashed sets: 574 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478174 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478174 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478174/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478174 Building REAL300025478175 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478175' /scratch/stefan/7787258/working/building/REAL300025478175 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478175 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478175/0 /scratch/stefan/7787258/working/building/REAL300025478175 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/29 `/scratch/stefan/7787258/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(C)(C)O1) `REAL300025478175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478175 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 62, 62, 62, 62, 62, 1, 14, 26, 26, 29, 29, 29, 29, 29, 29, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 62, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) 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: REAL300025478175 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 19, 29, 29, 29, 29, 44, 44, 76, 108, 201, 201, 201, 201, 201, 29, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 19, 29, 29, 29, 29, 29, 76, 76, 201, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [42, 43, 44, 45, 46, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52]) total number of confs: 527 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478175 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 134, 62, 62, 62, 62, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 62, 163, 199, 199, 201, 201, 201, 201, 201, 201, 163, 163, 163, 134, 134, 62, 62, 62, 62, 62, 36, 36, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478175 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478175 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478175/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478175 Building REAL300025478176 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478176' /scratch/stefan/7787258/working/building/REAL300025478176 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478176 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478176/0 /scratch/stefan/7787258/working/building/REAL300025478176 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/30 `/scratch/stefan/7787258/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=NN1C) `REAL300025478176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478176 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 52, 52, 52, 52, 52, 1, 14, 26, 26, 41, 48, 48, 48, 48, 48, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 11, 11, 52, 1, 1, 41, 41, 48, 48, 48, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 270 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: REAL300025478176 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 19, 36, 48, 48, 48, 48, 63, 63, 113, 133, 201, 201, 201, 201, 201, 48, 4, 12, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 36, 36, 48, 48, 48, 48, 48, 113, 113, 201, 48, 48, 4, 4, 1, 1, 2, 2, 2] 201 rigid atoms, others: [44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 624 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: REAL300025478176 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 99, 52, 52, 52, 52, 46, 40, 46, 13, 1, 1, 1, 1, 1, 1, 1, 52, 119, 161, 161, 175, 201, 201, 201, 201, 201, 119, 119, 119, 99, 99, 52, 52, 52, 52, 52, 40, 40, 1, 52, 52, 175, 175, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 750 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478176 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478176 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478176/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478176 Building REAL300025478177 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478177' /scratch/stefan/7787258/working/building/REAL300025478177 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478177 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478177/0 /scratch/stefan/7787258/working/building/REAL300025478177 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/31 `/scratch/stefan/7787258/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CSC1) `REAL300025478177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478177 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 19, 53, 53, 53, 53, 53, 1, 13, 23, 23, 25, 40, 40, 40, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 53, 1, 1, 25, 25, 40, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478177 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 12, 31, 40, 40, 40, 40, 53, 53, 110, 135, 201, 201, 201, 201, 201, 40, 4, 8, 1, 1, 1, 1, 1, 12, 12, 12, 31, 31, 40, 40, 40, 40, 40, 110, 110, 201, 40, 40, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 622 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478177 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 100, 53, 53, 53, 53, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 53, 127, 151, 151, 151, 201, 201, 201, 127, 127, 127, 100, 100, 53, 53, 53, 53, 53, 35, 35, 1, 53, 53, 151, 151, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478177 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478177 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478177/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478177 Building REAL300025478178 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478178' /scratch/stefan/7787258/working/building/REAL300025478178 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478178 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478178/0 /scratch/stefan/7787258/working/building/REAL300025478178 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/32 `/scratch/stefan/7787258/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CCC1) `REAL300025478178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478178 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 67, 67, 67, 67, 67, 1, 12, 25, 25, 31, 31, 31, 31, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 67, 1, 1, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478178 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 25, 31, 31, 31, 31, 46, 46, 89, 119, 201, 201, 201, 201, 201, 31, 1, 7, 1, 1, 1, 1, 1, 14, 14, 14, 25, 25, 31, 31, 31, 31, 31, 89, 89, 201, 31, 31, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 558 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478178 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 137, 67, 67, 67, 67, 45, 37, 45, 13, 1, 1, 1, 1, 1, 1, 1, 67, 165, 195, 195, 201, 201, 201, 201, 165, 165, 165, 137, 137, 67, 67, 67, 67, 67, 37, 37, 1, 67, 67, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478178 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478178 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478178/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478178 Building REAL300025478179 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478179' /scratch/stefan/7787258/working/building/REAL300025478179 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478179 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478179/0 /scratch/stefan/7787258/working/building/REAL300025478179 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/33 `/scratch/stefan/7787258/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CO) `REAL300025478179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478179 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 54, 54, 54, 54, 54, 1, 9, 20, 20, 38, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 54, 1, 1, 38, 38, 114] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 17, 35, 36, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478179 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 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: [132, 103, 54, 54, 54, 54, 32, 27, 32, 11, 1, 1, 1, 1, 1, 1, 1, 54, 132, 185, 185, 201, 132, 132, 132, 103, 103, 54, 54, 54, 54, 54, 27, 27, 1, 54, 54, 201, 201, 603] 603 rigid atoms, others: [34, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 1396 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478179 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478179 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478179/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478179 Building REAL300025478180 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478180' /scratch/stefan/7787258/working/building/REAL300025478180 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478180 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478180/0 /scratch/stefan/7787258/working/building/REAL300025478180 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/34 `/scratch/stefan/7787258/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC(N)=O) `REAL300025478180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478180 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 6, 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: [5, 3, 1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 37, 37, 37, 37, 37, 1, 5, 10, 10, 13, 13, 17, 17, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 9, 9, 37, 1, 1, 13, 13, 17, 17] 51 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 126 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478180 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 6, 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: [47, 46, 37, 37, 37, 37, 37, 32, 37, 13, 1, 1, 1, 1, 1, 1, 1, 37, 47, 51, 51, 51, 51, 51, 51, 47, 47, 47, 46, 46, 37, 37, 37, 37, 37, 32, 32, 1, 37, 37, 51, 51, 51, 51] 51 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 198 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478180 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478180 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478180/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478180 Building REAL300025478181 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478181' /scratch/stefan/7787258/working/building/REAL300025478181 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478181 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478181/0 /scratch/stefan/7787258/working/building/REAL300025478181 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/35 `/scratch/stefan/7787258/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C[N+]([O-])=C1) `REAL300025478181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478181 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C[N+]([O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 12, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 21, 68, 68, 68, 68, 68, 1, 16, 33, 33, 42, 42, 42, 42, 42, 42, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 68, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 236 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: REAL300025478181 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C[N+]([O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 12, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 15, 30, 42, 42, 42, 42, 61, 61, 106, 127, 201, 201, 201, 201, 201, 42, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 42, 42, 42, 42, 42, 106, 106, 201, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300025478181 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C[N+]([O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 12, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 130, 68, 68, 68, 68, 59, 48, 59, 13, 1, 1, 1, 1, 1, 1, 1, 68, 151, 191, 191, 201, 201, 201, 201, 201, 201, 151, 151, 151, 130, 130, 68, 68, 68, 68, 68, 48, 48, 1, 68, 68, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 760 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478181 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478181 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478181/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478181 Building REAL300025478182 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478182' /scratch/stefan/7787258/working/building/REAL300025478182 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478182 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478182/0 /scratch/stefan/7787258/working/building/REAL300025478182 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/36 `/scratch/stefan/7787258/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1) `REAL300025478182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478182 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 51, 51, 51, 51, 51, 1, 16, 22, 22, 29, 29, 29, 29, 29, 29, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 51, 1, 1, 29, 29, 29] 112 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478182 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 7, 12, 22, 29, 29, 29, 29, 32, 32, 58, 71, 112, 112, 112, 112, 112, 29, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 29, 29, 29, 29, 29, 58, 58, 112, 29, 29, 1, 1, 1] 112 rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478182 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 81, 51, 51, 51, 51, 47, 35, 47, 13, 1, 1, 1, 1, 1, 1, 1, 51, 103, 109, 109, 112, 112, 112, 112, 112, 112, 103, 103, 103, 81, 81, 51, 51, 51, 51, 51, 35, 35, 1, 51, 51, 112, 112, 112] 112 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478182 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478182 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478182/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478182 Building REAL300025478183 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478183' /scratch/stefan/7787258/working/building/REAL300025478183 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478183 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478183/0 /scratch/stefan/7787258/working/building/REAL300025478183 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/37 `/scratch/stefan/7787258/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478183 none C#CCSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 21, 15, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 55, 55, 55, 55, 55, 1, 38, 38, 38, 15, 15, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 12, 12, 55, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478183 none C#CCSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 152, 116, 116, 116, 107, 116, 55, 55, 55, 55, 40, 32, 40, 13, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 152, 152, 116, 116, 116, 107, 107, 55, 55, 55, 55, 55, 32, 32, 1, 55, 55] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 918 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478183 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478183 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478183/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478183 Building REAL300025478184 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478184' /scratch/stefan/7787258/working/building/REAL300025478184 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478184 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478184/0 /scratch/stefan/7787258/working/building/REAL300025478184 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/38 `/scratch/stefan/7787258/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478184 none CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 22, 33, 13, 22, 5, 13, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 66, 66, 66, 66, 66, 1, 33, 33, 33, 33, 99, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 66, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 327 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478184 none CC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 194, 201, 166, 194, 110, 166, 66, 66, 66, 66, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 603, 166, 166, 166, 110, 110, 66, 66, 66, 66, 66, 35, 35, 1, 66, 66] 603 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 1357 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478184 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478184 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478184/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478184 Building REAL300025478185 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478185' /scratch/stefan/7787258/working/building/REAL300025478185 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478185 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478185/0 /scratch/stefan/7787258/working/building/REAL300025478185 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/39 `/scratch/stefan/7787258/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCC1) `REAL300025478185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478185 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 62, 62, 62, 62, 62, 1, 12, 23, 23, 29, 29, 29, 29, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 62, 1, 1, 87, 29, 29, 29, 29, 29, 29] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478185 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [10, 6, 10, 23, 29, 29, 29, 29, 48, 48, 86, 114, 201, 201, 201, 201, 201, 29, 1, 6, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 29, 29, 29, 29, 29, 86, 86, 201, 29, 29, 6, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 555 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478185 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [161, 130, 62, 62, 62, 62, 47, 39, 47, 13, 1, 1, 1, 1, 1, 1, 1, 62, 161, 199, 199, 201, 201, 201, 201, 161, 161, 161, 130, 130, 62, 62, 62, 62, 62, 39, 39, 1, 62, 62, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1360 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478185 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478185 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478185/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478185 Building REAL300025478186 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478186' /scratch/stefan/7787258/working/building/REAL300025478186 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478186 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478186/0 /scratch/stefan/7787258/working/building/REAL300025478186 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/40 `/scratch/stefan/7787258/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CC1) `REAL300025478186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478186 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 14, 23, 76, 76, 76, 76, 76, 1, 10, 18, 18, 23, 23, 35, 35, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 14, 14, 76, 1, 1, 23, 69, 35, 35, 35, 35, 35] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 334 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478186 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [19, 13, 19, 31, 35, 35, 35, 35, 52, 52, 91, 120, 201, 201, 201, 201, 201, 35, 5, 13, 1, 5, 1, 1, 1, 19, 19, 19, 31, 31, 35, 35, 35, 35, 35, 91, 91, 201, 35, 35, 5, 15, 1, 1, 1, 1, 1] 603 rigid atoms, others: [42, 43, 44, 45, 46, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 575 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478186 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 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: [148, 132, 76, 76, 76, 76, 51, 40, 51, 13, 1, 1, 1, 1, 1, 1, 1, 76, 148, 174, 174, 178, 178, 201, 201, 148, 148, 148, 132, 132, 76, 76, 76, 76, 76, 40, 40, 1, 76, 76, 178, 534, 201, 201, 201, 201, 201] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1305 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478186 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478186 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478186/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478186 Building REAL300025478187 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478187' /scratch/stefan/7787258/working/building/REAL300025478187 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478187 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478187/0 /scratch/stefan/7787258/working/building/REAL300025478187 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/41 `/scratch/stefan/7787258/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C(N)=O)CCC1) `REAL300025478187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478187 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C(N)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 46, 46, 46, 46, 46, 1, 13, 22, 22, 23, 23, 23, 23, 23, 23, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478187 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C(N)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 15, 23, 23, 23, 23, 34, 34, 62, 103, 201, 201, 201, 201, 201, 23, 1, 3, 1, 1, 3, 3, 1, 1, 1, 5, 5, 5, 15, 15, 23, 23, 23, 23, 23, 62, 62, 201, 23, 23, 3, 3, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478187 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C(N)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 110, 46, 46, 46, 46, 33, 25, 33, 12, 1, 1, 1, 1, 1, 1, 1, 46, 140, 195, 195, 201, 201, 201, 201, 201, 201, 140, 140, 140, 110, 110, 46, 46, 46, 46, 46, 25, 25, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 751 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478187 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478187 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478187/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478187 Building REAL300025478188 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478188' /scratch/stefan/7787258/working/building/REAL300025478188 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478188 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478188/0 /scratch/stefan/7787258/working/building/REAL300025478188 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/42 `/scratch/stefan/7787258/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NN=C1) `REAL300025478188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478188 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 19, 55, 55, 55, 55, 55, 1, 12, 23, 23, 35, 41, 41, 41, 41, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 35, 35, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 255 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478188 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 28, 38, 38, 38, 38, 66, 66, 96, 125, 201, 201, 201, 201, 201, 38, 5, 13, 1, 1, 1, 1, 1, 1, 17, 17, 17, 28, 28, 38, 38, 38, 38, 38, 96, 96, 201, 38, 38, 5, 5, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 570 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: REAL300025478188 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 108, 55, 55, 55, 55, 49, 43, 49, 13, 1, 1, 1, 1, 1, 1, 1, 55, 139, 179, 179, 201, 201, 201, 201, 201, 139, 139, 139, 108, 108, 55, 55, 55, 55, 55, 43, 43, 1, 55, 55, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 830 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478188 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478188 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478188/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478188 Building REAL300025478189 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478189' /scratch/stefan/7787258/working/building/REAL300025478189 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478189 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478189/0 /scratch/stefan/7787258/working/building/REAL300025478189 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/43 `/scratch/stefan/7787258/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478189 none C=CCC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 10, 20, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 67, 67, 67, 67, 67, 1, 45, 45, 45, 28, 28, 20, 20, 20, 20, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 14, 14, 67, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 311 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478189 none C=CCC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 117, 187, 117, 117, 109, 117, 67, 67, 67, 67, 51, 40, 51, 12, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 187, 187, 187, 187, 117, 117, 117, 109, 109, 67, 67, 67, 67, 67, 40, 40, 1, 67, 67] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 932 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478189 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478189 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478189/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478189 Building REAL300025478190 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478190' /scratch/stefan/7787258/working/building/REAL300025478190 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478190 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478190/0 /scratch/stefan/7787258/working/building/REAL300025478190 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/44 `/scratch/stefan/7787258/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1F) `REAL300025478190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478190 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 35, 35, 35, 35, 35, 1, 9, 17, 17, 29, 29, 29, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 35, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478190 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 19, 29, 29, 29, 29, 36, 36, 59, 91, 201, 201, 201, 201, 201, 29, 1, 5, 1, 1, 1, 1, 9, 9, 9, 19, 19, 29, 29, 29, 29, 29, 59, 59, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300025478190 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 68, 35, 35, 35, 35, 23, 21, 23, 11, 1, 1, 1, 1, 1, 1, 1, 35, 96, 139, 139, 201, 201, 201, 96, 96, 96, 68, 68, 35, 35, 35, 35, 35, 21, 21, 1, 35, 35, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478190 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478190 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478190/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478190 Building REAL300025478191 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478191' /scratch/stefan/7787258/working/building/REAL300025478191 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478191 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478191/0 /scratch/stefan/7787258/working/building/REAL300025478191 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/45 `/scratch/stefan/7787258/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1(C)CCC1) `REAL300025478191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478191 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 58, 58, 58, 58, 58, 1, 11, 17, 17, 23, 32, 43, 43, 43, 43, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1, 23, 23, 43, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478191 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 15, 18, 32, 43, 43, 43, 43, 56, 56, 82, 109, 201, 201, 201, 201, 201, 43, 8, 15, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 32, 32, 43, 43, 43, 43, 43, 82, 82, 201, 43, 43, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 52, 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]) total number of confs: 536 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478191 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 109, 58, 58, 58, 58, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 58, 121, 131, 131, 153, 197, 201, 201, 201, 201, 121, 121, 121, 109, 109, 58, 58, 58, 58, 58, 35, 35, 1, 58, 58, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478191 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478191 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478191/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478191 Building REAL300025478192 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478192' /scratch/stefan/7787258/working/building/REAL300025478192 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478192 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478192/0 /scratch/stefan/7787258/working/building/REAL300025478192 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/46 `/scratch/stefan/7787258/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478192 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 6, 7, 16, 16, 16, 16, 16, 1, 6, 7, 7, 7, 6, 6, 6, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 6, 6, 16, 1, 1, 7, 7, 7, 7, 7, 7] 16 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 65 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: REAL300025478192 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 16, 11, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 1, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 40 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478192 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478192/1 /scratch/stefan/7787258/working/building/REAL300025478192 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/47 `/scratch/stefan/7787258/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C) `REAL300025478192.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478192 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 19, 40, 15, 19, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 73, 73, 73, 73, 73, 1, 40, 47, 47, 40, 40, 40, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 14, 14, 73, 1, 1, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 316 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: REAL300025478192 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 179, 186, 155, 179, 73, 73, 73, 73, 49, 38, 49, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 179, 179, 179, 155, 155, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 807 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478192 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478192 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478192/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478192/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478192 Building REAL300025478193 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478193' /scratch/stefan/7787258/working/building/REAL300025478193 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478193 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478193/0 /scratch/stefan/7787258/working/building/REAL300025478193 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/48 `/scratch/stefan/7787258/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCF) `REAL300025478193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478193 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 56, 56, 56, 56, 56, 1, 10, 21, 21, 22, 24, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1, 22, 22, 24, 24] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 17, 37, 36, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478193 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 97, 56, 56, 56, 56, 38, 32, 38, 12, 1, 1, 1, 1, 1, 1, 1, 56, 140, 199, 199, 201, 201, 140, 140, 140, 97, 97, 56, 56, 56, 56, 56, 32, 32, 1, 56, 56, 201, 201, 201, 201] 201 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478193 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478193 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478193/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478193 Building REAL300025478194 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478194' /scratch/stefan/7787258/working/building/REAL300025478194 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478194 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478194/0 /scratch/stefan/7787258/working/building/REAL300025478194 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/49 `/scratch/stefan/7787258/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=CN=N1) `REAL300025478194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478194 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 63, 63, 63, 63, 63, 1, 13, 23, 23, 33, 40, 40, 40, 40, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 33, 33, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 261 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: REAL300025478194 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 35, 40, 40, 40, 40, 64, 64, 102, 133, 201, 201, 201, 201, 201, 40, 7, 15, 1, 1, 1, 1, 1, 1, 23, 23, 23, 35, 35, 40, 40, 40, 40, 40, 102, 102, 201, 40, 40, 7, 7, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 593 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: REAL300025478194 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 1, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 126, 63, 63, 63, 63, 48, 41, 48, 13, 1, 1, 1, 1, 1, 1, 1, 63, 153, 181, 181, 192, 201, 201, 201, 201, 153, 153, 153, 126, 126, 63, 63, 63, 63, 63, 41, 41, 1, 63, 63, 192, 192, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 796 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478194 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478194 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478194/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478194 Building REAL300025478195 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478195' /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478195 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478195/0 /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/50 `/scratch/stefan/7787258/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@@H+]1C) `REAL300025478195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 14, 14, 14, 14, 14, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 7, 7, 14, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 17 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 7, 8, 8, 8, 8, 9, 9, 13, 14, 17, 17, 17, 17, 17, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 13, 13, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 52, 53, 54]) total number of confs: 71 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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 14, 14, 14, 14, 14, 13, 14, 10, 1, 1, 1, 1, 1, 1, 1, 14, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 15, 15, 14, 14, 14, 14, 14, 13, 13, 1, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 47 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478195/1 /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/51 `/scratch/stefan/7787258/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@H+]1C) `REAL300025478195.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 1, 1, 1, 1, 1, 1, 5, 5, 9, 14, 21, 21, 21, 21, 21, 1, 9, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 9, 9, 21, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 26 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 8, 11, 11, 11, 11, 15, 15, 22, 24, 26, 26, 26, 26, 26, 11, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 11, 11, 11, 11, 11, 22, 22, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 52, 53, 54]) total number of confs: 105 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: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 21, 21, 21, 21, 21, 20, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 24, 21, 21, 21, 21, 21, 20, 20, 1, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478195/2 /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/52 `/scratch/stefan/7787258/working/3D/52' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCCN1C) `REAL300025478195.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478195/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 66, 66, 66, 66, 66, 1, 16, 30, 30, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 14, 14, 66, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 21, 33, 33, 33, 33, 48, 48, 86, 116, 201, 201, 201, 201, 201, 33, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 33, 33, 33, 33, 33, 86, 86, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 51, 52, 53]) total number of confs: 545 number of broken/clashed sets: 156 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478195 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 136, 66, 66, 66, 66, 44, 36, 44, 12, 1, 1, 1, 1, 1, 1, 1, 66, 159, 200, 200, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 136, 136, 66, 66, 66, 66, 66, 36, 36, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 764 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478195 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478195 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478195/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478195/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478195/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478195 Building REAL300025478196 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478196' /scratch/stefan/7787258/working/building/REAL300025478196 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478196 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478196/0 /scratch/stefan/7787258/working/building/REAL300025478196 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/53 `/scratch/stefan/7787258/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478196 none C=CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 3, 3, 5, 5, 19, 32, 32, 32, 32, 43, 43, 68, 109, 201, 201, 201, 201, 201, 32, 1, 1, 1, 5, 5, 5, 5, 5, 5, 19, 19, 32, 32, 32, 32, 32, 68, 68, 201, 32, 32, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478196 none C=CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 125, 137, 107, 125, 49, 49, 49, 49, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 201, 125, 125, 125, 107, 107, 49, 49, 49, 49, 49, 25, 25, 1, 49, 49, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 799 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478196 none C=CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 23, 14, 23, 6, 14, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 49, 49, 49, 49, 49, 1, 32, 32, 32, 35, 35, 35, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478196 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478196 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478196/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478196 Building REAL300025478197 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478197' /scratch/stefan/7787258/working/building/REAL300025478197 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478197 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478197/0 /scratch/stefan/7787258/working/building/REAL300025478197 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/54 `/scratch/stefan/7787258/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)COC1) `REAL300025478197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478197 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 3, 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: [12, 6, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 53, 53, 53, 53, 53, 1, 12, 24, 24, 24, 24, 24, 24, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 72, 24, 24, 24, 24] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478197 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 3, 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, 3, 6, 16, 24, 24, 24, 24, 35, 35, 57, 88, 201, 201, 201, 201, 201, 24, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 24, 24, 24, 24, 24, 57, 57, 201, 24, 24, 6, 1, 1, 1, 1] 603 rigid atoms, others: [41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 514 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478197 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 3, 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: [139, 102, 53, 53, 53, 53, 35, 29, 35, 13, 1, 1, 1, 1, 1, 1, 1, 53, 139, 201, 201, 201, 201, 201, 201, 139, 139, 139, 102, 102, 53, 53, 53, 53, 53, 29, 29, 1, 53, 53, 603, 201, 201, 201, 201] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1337 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478197 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478197 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478197/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478197 Building REAL300025478198 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478198' /scratch/stefan/7787258/working/building/REAL300025478198 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478198 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478198/0 /scratch/stefan/7787258/working/building/REAL300025478198 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/55 `/scratch/stefan/7787258/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478198 none CCC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 39, 29, 39, 17, 29, 14, 17, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 62, 62, 62, 62, 62, 1, 40, 40, 40, 40, 40, 39, 39, 39, 39, 29, 87, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 62, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 380 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478198 none CCC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 189, 201, 128, 189, 124, 128, 108, 124, 62, 62, 62, 62, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 567, 124, 124, 124, 108, 108, 62, 62, 62, 62, 62, 37, 37, 1, 62, 62] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1478 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478198 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478198 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478198/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478198 Building REAL300025478199 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478199' /scratch/stefan/7787258/working/building/REAL300025478199 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478199 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478199/0 /scratch/stefan/7787258/working/building/REAL300025478199 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/56 `/scratch/stefan/7787258/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CC1) `REAL300025478199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478199 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 18, 14, 18, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 65, 65, 65, 65, 65, 1, 29, 29, 29, 29, 29, 29, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 65, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 218 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478199 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 9, 9, 18, 29, 29, 29, 29, 45, 45, 78, 112, 201, 201, 201, 201, 201, 29, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 18, 29, 29, 29, 29, 29, 78, 78, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 22, 23, 24] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 524 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: REAL300025478199 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 136, 139, 127, 136, 65, 65, 65, 65, 49, 38, 49, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 136, 136, 136, 127, 127, 65, 65, 65, 65, 65, 38, 38, 1, 65, 65, 201, 201, 201, 201] 201 rigid atoms, others: [40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 785 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478199 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478199 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478199/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478199 Building REAL300025478200 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478200' /scratch/stefan/7787258/working/building/REAL300025478200 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478200 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478200/0 /scratch/stefan/7787258/working/building/REAL300025478200 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/57 `/scratch/stefan/7787258/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NN=N1) `REAL300025478200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478200 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 14, 19, 6, 14, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 83, 83, 83, 83, 83, 1, 25, 32, 32, 32, 32, 25, 25, 25, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 16, 16, 83, 1, 1, 32] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46]) total number of confs: 255 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: REAL300025478200 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 6, 6, 10, 10, 20, 32, 32, 32, 32, 57, 57, 95, 121, 201, 201, 201, 201, 201, 32, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 20, 20, 32, 32, 32, 32, 32, 95, 95, 201, 32, 32, 1] 201 rigid atoms, others: [1, 46, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 554 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: REAL300025478200 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 201, 188, 190, 170, 188, 83, 83, 83, 83, 54, 44, 54, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 170, 170, 83, 83, 83, 83, 83, 44, 44, 1, 83, 83, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 802 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478200 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478200 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478200/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478200 Building REAL300025478201 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478201' /scratch/stefan/7787258/working/building/REAL300025478201 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478201 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478201/0 /scratch/stefan/7787258/working/building/REAL300025478201 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/58 `/scratch/stefan/7787258/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCN1N=O) `REAL300025478201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478201 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCN1N=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 8, 8, 11, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 82, 82, 82, 82, 82, 1, 11, 18, 18, 20, 20, 20, 20, 20, 24, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 16, 16, 82, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 221 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: REAL300025478201 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCN1N=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 8, 8, 11, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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: [11, 5, 11, 16, 20, 20, 20, 20, 41, 41, 72, 107, 201, 201, 201, 201, 201, 20, 1, 5, 1, 1, 1, 1, 1, 1, 3, 11, 11, 11, 16, 16, 20, 20, 20, 20, 20, 72, 72, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 491 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: REAL300025478201 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCN1N=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 8, 8, 11, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 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: [174, 150, 82, 82, 82, 82, 59, 46, 59, 13, 1, 1, 1, 1, 1, 1, 1, 82, 174, 199, 199, 201, 201, 201, 201, 201, 201, 174, 174, 174, 150, 150, 82, 82, 82, 82, 82, 46, 46, 1, 82, 82, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 776 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478201 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478201 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478201/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478201 Building REAL300025478202 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478202' /scratch/stefan/7787258/working/building/REAL300025478202 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478202 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478202/0 /scratch/stefan/7787258/working/building/REAL300025478202 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/59 `/scratch/stefan/7787258/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478202 none CCC1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 31, 31, 31, 31, 43, 43, 74, 101, 201, 201, 201, 201, 201, 31, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 8, 20, 20, 31, 31, 31, 31, 31, 74, 74, 201, 31, 31] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478202 none CCC1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 131, 129, 131, 113, 129, 56, 56, 56, 56, 45, 37, 45, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 113, 113, 56, 56, 56, 56, 56, 37, 37, 1, 56, 56] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 782 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478202 none CCC1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 31, 31, 31, 15, 12, 15, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 56, 56, 56, 56, 56, 1, 39, 39, 39, 39, 39, 31, 31, 31, 31, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 56, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478202 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478202 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478202/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478202 Building REAL300025478203 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478203' /scratch/stefan/7787258/working/building/REAL300025478203 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478203 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478203/0 /scratch/stefan/7787258/working/building/REAL300025478203 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/60 `/scratch/stefan/7787258/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478203 none CC(O)CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 30, 44, 29, 27, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 47, 47, 47, 47, 47, 1, 44, 44, 44, 44, 132, 30, 30, 30, 30, 27, 27, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 9, 9, 47, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 426 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478203 none CC(O)CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 167, 201, 167, 165, 112, 112, 112, 90, 112, 47, 47, 47, 47, 36, 26, 36, 12, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 603, 167, 167, 167, 167, 165, 165, 112, 112, 112, 90, 90, 47, 47, 47, 47, 47, 26, 26, 1, 47, 47] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1544 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478203 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478203 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478203/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478203 Building REAL300025478204 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478204' /scratch/stefan/7787258/working/building/REAL300025478204 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478204 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478204/0 /scratch/stefan/7787258/working/building/REAL300025478204 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/61 `/scratch/stefan/7787258/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478204 none CC1=NOC(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 32, 46, 46, 46, 46, 60, 60, 104, 128, 201, 201, 201, 201, 201, 46, 1, 2, 2, 2, 8, 8, 17, 17, 17, 32, 32, 46, 46, 46, 46, 46, 104, 104, 201, 46, 46, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478204 none CC1=NOC(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 187, 126, 126, 126, 103, 126, 54, 54, 54, 54, 43, 34, 43, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 187, 187, 126, 126, 126, 103, 103, 54, 54, 54, 54, 54, 34, 34, 1, 54, 54, 201] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 822 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478204 none CC1=NOC(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 29, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 54, 54, 54, 54, 54, 1, 46, 46, 46, 46, 29, 29, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 54, 1, 1, 46] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478204 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478204 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478204/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478204 Building REAL300025478205 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478205' /scratch/stefan/7787258/working/building/REAL300025478205 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478205 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478205/0 /scratch/stefan/7787258/working/building/REAL300025478205 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/62 `/scratch/stefan/7787258/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CC1) `REAL300025478205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478205 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 19, 65, 65, 65, 65, 65, 1, 13, 25, 25, 38, 43, 43, 43, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 65, 1, 1, 38, 38, 129, 43, 43, 43, 43] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 411 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478205 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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: [17, 12, 17, 31, 43, 43, 43, 43, 52, 52, 96, 120, 201, 201, 201, 201, 201, 43, 6, 12, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 43, 43, 43, 43, 43, 96, 96, 201, 43, 43, 6, 6, 6, 1, 1, 1, 1] 603 rigid atoms, others: [43, 44, 45, 46, 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, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 602 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478205 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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: [143, 118, 65, 65, 65, 65, 50, 39, 50, 13, 1, 1, 1, 1, 1, 1, 1, 65, 143, 171, 171, 201, 201, 201, 201, 143, 143, 143, 118, 118, 65, 65, 65, 65, 65, 39, 39, 1, 65, 65, 201, 201, 603, 201, 201, 201, 201] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1432 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478205 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478205 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478205/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478205 Building REAL300025478206 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478206' /scratch/stefan/7787258/working/building/REAL300025478206 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478206 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478206/0 /scratch/stefan/7787258/working/building/REAL300025478206 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/63 `/scratch/stefan/7787258/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCOCC21) `REAL300025478206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478206 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCOCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 60, 60, 60, 60, 60, 1, 15, 27, 27, 35, 35, 35, 35, 35, 35, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 13, 13, 60, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478206 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCOCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 22, 35, 35, 35, 35, 53, 53, 90, 119, 201, 201, 201, 201, 201, 35, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 22, 22, 35, 35, 35, 35, 35, 90, 90, 201, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 554 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478206 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCOCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 123, 60, 60, 60, 60, 46, 38, 46, 12, 1, 1, 1, 1, 1, 1, 1, 60, 141, 173, 173, 201, 201, 201, 201, 201, 201, 141, 141, 141, 123, 123, 60, 60, 60, 60, 60, 38, 38, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478206 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478206 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478206/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478206 Building REAL300025478207 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478207' /scratch/stefan/7787258/working/building/REAL300025478207 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478207 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478207/0 /scratch/stefan/7787258/working/building/REAL300025478207 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/64 `/scratch/stefan/7787258/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCF) `REAL300025478207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478207 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 72, 72, 72, 72, 72, 1, 12, 23, 23, 31, 31, 33, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1, 31, 31, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 240 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: REAL300025478207 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 144, 72, 72, 72, 72, 51, 42, 51, 13, 1, 1, 1, 1, 1, 1, 1, 72, 170, 189, 189, 201, 201, 201, 170, 170, 170, 144, 144, 72, 72, 72, 72, 72, 42, 42, 1, 72, 72, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 781 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478207 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478207 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478207/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478207 Building REAL300025478208 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478208' /scratch/stefan/7787258/working/building/REAL300025478208 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478208 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478208/0 /scratch/stefan/7787258/working/building/REAL300025478208 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/65 `/scratch/stefan/7787258/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)CC1CC1) `REAL300025478208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478208 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 18, 67, 67, 67, 67, 67, 1, 11, 18, 18, 18, 18, 27, 42, 42, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 1, 1, 18, 27, 27, 42, 42, 42, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) 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: REAL300025478208 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 29, 42, 42, 42, 42, 59, 59, 93, 115, 201, 201, 201, 201, 201, 42, 9, 13, 3, 9, 1, 1, 1, 1, 15, 15, 15, 29, 29, 42, 42, 42, 42, 42, 93, 93, 201, 42, 42, 9, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 579 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: REAL300025478208 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 132, 67, 67, 67, 67, 54, 44, 54, 13, 1, 1, 1, 1, 1, 1, 1, 67, 149, 172, 172, 172, 172, 180, 201, 201, 149, 149, 149, 132, 132, 67, 67, 67, 67, 67, 44, 44, 1, 67, 67, 172, 180, 180, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 791 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478208 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478208 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478208/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478208 Building REAL300025478209 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478209' /scratch/stefan/7787258/working/building/REAL300025478209 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478209 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478209/0 /scratch/stefan/7787258/working/building/REAL300025478209 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/66 `/scratch/stefan/7787258/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478209 none CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 60, 60, 60, 60, 60, 1, 35, 37, 37, 35, 35, 35, 35, 35, 35, 26, 26, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 13, 13, 60, 1, 1, 37, 37, 37, 37, 37] 201 rigid atoms, others: [43, 49, 8, 9, 10, 11, 12, 13, 44, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478209 none CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 7, 16, 16, 16, 16, 28, 37, 37, 37, 37, 48, 48, 83, 111, 201, 201, 201, 201, 201, 37, 1, 1, 1, 6, 6, 6, 6, 6, 3, 7, 7, 16, 16, 16, 28, 28, 37, 37, 37, 37, 37, 83, 83, 201, 37, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 50, 51, 52, 53, 54, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 554 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478209 none CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 185, 102, 102, 102, 98, 102, 60, 60, 60, 60, 48, 38, 48, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 102, 102, 102, 98, 98, 60, 60, 60, 60, 60, 38, 38, 1, 60, 60, 201, 201, 201, 201, 201] 201 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478209 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478209 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478209/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478209 Building REAL300025478210 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478210' /scratch/stefan/7787258/working/building/REAL300025478210 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478210 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478210/0 /scratch/stefan/7787258/working/building/REAL300025478210 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/67 `/scratch/stefan/7787258/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1) `REAL300025478210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478210 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 3, 3, 6, 9, 25, 25, 25, 25, 25, 1, 5, 6, 6, 9, 9, 11, 11, 11, 11, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 6, 6, 25, 1, 1, 9, 9, 11, 11, 11] 31 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 80 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: REAL300025478210 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 7, 8, 8, 8, 8, 9, 9, 15, 21, 25, 25, 25, 25, 25, 8, 2, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 15, 15, 25, 8, 8, 2, 2, 1, 1, 1] 25 rigid atoms, others: [44, 45, 46, 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]) total number of confs: 84 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478210 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 25, 25, 25, 25, 25, 23, 25, 12, 1, 1, 1, 1, 1, 1, 1, 25, 30, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 30, 30, 30, 25, 25, 25, 25, 25, 23, 23, 1, 25, 25, 31, 31, 31, 31, 31] 31 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478210 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478210 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478210/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478210 Building REAL300025478211 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478211' /scratch/stefan/7787258/working/building/REAL300025478211 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478211 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478211/0 /scratch/stefan/7787258/working/building/REAL300025478211 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/68 `/scratch/stefan/7787258/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478211 none CNC(=O)N[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 40, 40, 40, 28, 14, 28, 28, 12, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 73, 73, 73, 73, 73, 1, 47, 47, 47, 47, 40, 28, 28, 28, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 73, 1, 1] 201 rigid atoms, others: [45, 49, 41, 42, 43, 12, 13, 14, 15, 16, 17, 50, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 306 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478211 none CNC(=O)N[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 165, 188, 188, 162, 165, 132, 162, 73, 73, 73, 73, 57, 42, 57, 12, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 188, 188, 188, 162, 162, 162, 132, 132, 73, 73, 73, 73, 73, 42, 42, 1, 73, 73] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 822 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478211 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478211 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478211/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478211 Building REAL300025478212 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478212' /scratch/stefan/7787258/working/building/REAL300025478212 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478212 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478212/0 /scratch/stefan/7787258/working/building/REAL300025478212 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/69 `/scratch/stefan/7787258/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OC) `REAL300025478212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478212 none CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 31, 16, 13, 16, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 17, 26, 73, 73, 73, 73, 73, 1, 36, 36, 36, 36, 36, 36, 36, 36, 31, 31, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 17, 17, 73, 1, 1, 36, 36, 36] 201 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478212 none CCC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 180, 176, 180, 144, 176, 73, 73, 73, 73, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 176, 176, 176, 144, 144, 73, 73, 73, 73, 73, 42, 42, 1, 73, 73, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478212 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478212 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478212/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478212 Building REAL300025478213 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478213' /scratch/stefan/7787258/working/building/REAL300025478213 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478213 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478213/0 /scratch/stefan/7787258/working/building/REAL300025478213 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/70 `/scratch/stefan/7787258/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CC1) `REAL300025478213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478213 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 15, 58, 58, 58, 58, 58, 1, 12, 27, 27, 42, 42, 42, 42, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1, 42, 42, 42, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478213 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 19, 31, 42, 42, 42, 42, 60, 60, 103, 121, 201, 201, 201, 201, 201, 42, 1, 10, 1, 1, 1, 1, 1, 19, 19, 19, 31, 31, 42, 42, 42, 42, 42, 103, 103, 201, 42, 42, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 580 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478213 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 58, 58, 58, 58, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 58, 142, 171, 171, 201, 201, 201, 201, 142, 142, 142, 117, 117, 58, 58, 58, 58, 58, 39, 39, 1, 58, 58, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 739 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478213 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478213 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478213/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478213 Building REAL300025478214 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478214' /scratch/stefan/7787258/working/building/REAL300025478214 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478214 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478214/0 /scratch/stefan/7787258/working/building/REAL300025478214 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/71 `/scratch/stefan/7787258/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=NN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478214 none CC1=NN=NN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 13, 13, 30, 47, 47, 47, 47, 72, 72, 116, 135, 201, 201, 201, 201, 201, 47, 2, 2, 2, 4, 4, 14, 14, 14, 30, 30, 47, 47, 47, 47, 47, 116, 116, 201, 47, 47] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478214 none CC1=NN=NN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 198, 154, 153, 154, 117, 153, 63, 63, 63, 63, 53, 45, 53, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 198, 198, 153, 153, 153, 117, 117, 63, 63, 63, 63, 63, 45, 45, 1, 63, 63] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 843 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478214 none CC1=NN=NN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 42, 12, 11, 12, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 63, 63, 63, 63, 63, 1, 47, 47, 47, 42, 42, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 63, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478214 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478214 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478214/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478214 Building REAL300025478215 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478215' /scratch/stefan/7787258/working/building/REAL300025478215 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478215 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478215/0 /scratch/stefan/7787258/working/building/REAL300025478215 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/72 `/scratch/stefan/7787258/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](F)C2) `REAL300025478215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478215 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 50, 50, 50, 50, 50, 1, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 7, 7, 50, 1, 1, 29, 29, 29, 29] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478215 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 18, 29, 29, 29, 29, 39, 39, 66, 104, 201, 201, 201, 201, 201, 29, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 29, 29, 29, 29, 29, 66, 66, 201, 29, 29, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478215 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 50, 50, 50, 50, 39, 30, 39, 13, 1, 1, 1, 1, 1, 1, 1, 50, 152, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 120, 120, 50, 50, 50, 50, 50, 30, 30, 1, 50, 50, 201, 201, 201, 201] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478215 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478215 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478215/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478215 Building REAL300025478216 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478216' /scratch/stefan/7787258/working/building/REAL300025478216 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478216 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478216/0 /scratch/stefan/7787258/working/building/REAL300025478216 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/73 `/scratch/stefan/7787258/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCOC1) `REAL300025478216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478216 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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: [12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 57, 57, 57, 57, 57, 1, 12, 27, 27, 33, 33, 33, 33, 33, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 57, 1, 1, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478216 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 10, 23, 33, 33, 33, 33, 52, 52, 90, 116, 201, 201, 201, 201, 201, 33, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 33, 33, 33, 33, 33, 90, 90, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478216 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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: [151, 128, 57, 57, 57, 57, 46, 39, 46, 13, 1, 1, 1, 1, 1, 1, 1, 57, 151, 190, 190, 201, 201, 201, 201, 201, 151, 151, 151, 128, 128, 57, 57, 57, 57, 57, 39, 39, 1, 57, 57, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478216 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478216 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478216/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478216 Building REAL300025478217 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478217' /scratch/stefan/7787258/working/building/REAL300025478217 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478217 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478217/0 /scratch/stefan/7787258/working/building/REAL300025478217 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/74 `/scratch/stefan/7787258/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC1(F)F) `REAL300025478217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478217 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 55, 55, 55, 55, 55, 1, 11, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 9, 9, 55, 1, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478217 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 13, 21, 21, 21, 21, 30, 30, 56, 80, 201, 201, 201, 201, 201, 21, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 21, 21, 21, 21, 21, 56, 56, 201, 21, 21, 2, 2, 2, 1, 1] 201 rigid atoms, others: [44, 45, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 489 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478217 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 117, 55, 55, 55, 55, 38, 33, 38, 13, 1, 1, 1, 1, 1, 1, 1, 55, 157, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 117, 117, 55, 55, 55, 55, 55, 33, 33, 1, 55, 55, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478217 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478217 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478217/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478217 Building REAL300025478218 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478218' /scratch/stefan/7787258/working/building/REAL300025478218 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478218 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478218/0 /scratch/stefan/7787258/working/building/REAL300025478218 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/75 `/scratch/stefan/7787258/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478218 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 19, 19, 19, 19, 26, 26, 42, 59, 117, 117, 117, 117, 117, 19, 1, 4, 4, 4, 4, 4, 5, 5, 5, 10, 10, 19, 19, 19, 19, 19, 42, 42, 117, 19, 19, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 47, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478218 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 117, 117, 117, 115, 115, 115, 97, 115, 52, 52, 52, 52, 37, 33, 37, 13, 1, 1, 1, 1, 1, 1, 1, 52, 117, 201, 201, 201, 201, 201, 115, 115, 115, 97, 97, 52, 52, 52, 52, 52, 33, 33, 1, 52, 52, 117] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 940 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478218 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 19, 19, 19, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 4, 4, 10, 15, 52, 52, 52, 52, 52, 1, 19, 35, 35, 35, 35, 35, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 52, 1, 1, 19] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478218 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478218 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478218/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478218 Building REAL300025478219 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478219' /scratch/stefan/7787258/working/building/REAL300025478219 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478219 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478219/0 /scratch/stefan/7787258/working/building/REAL300025478219 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/76 `/scratch/stefan/7787258/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C(C)(C)C) `REAL300025478219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478219 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 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: [16, 6, 1, 1, 1, 1, 1, 1, 6, 6, 17, 28, 84, 84, 84, 84, 84, 1, 16, 21, 21, 22, 22, 22, 22, 22, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 17, 17, 84, 1, 1, 22, 66, 22, 22, 22, 22, 22, 22, 22, 22, 22] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 459 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478219 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 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: [200, 155, 84, 84, 84, 84, 54, 45, 54, 13, 1, 1, 1, 1, 1, 1, 1, 84, 200, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 155, 155, 84, 84, 84, 84, 84, 45, 45, 1, 84, 84, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1368 number of broken/clashed sets: 459 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478219 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478219 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478219/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478219 Building REAL300025478220 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478220' /scratch/stefan/7787258/working/building/REAL300025478220 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478220 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478220/0 /scratch/stefan/7787258/working/building/REAL300025478220 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/77 `/scratch/stefan/7787258/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSCC1) `REAL300025478220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478220 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 16, 25, 72, 72, 72, 72, 72, 1, 15, 26, 26, 37, 37, 37, 37, 37, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 16, 16, 72, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 259 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478220 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 28, 37, 37, 37, 37, 47, 47, 92, 114, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 28, 28, 37, 37, 37, 37, 37, 92, 92, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 564 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478220 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 72, 72, 72, 72, 53, 40, 53, 13, 1, 1, 1, 1, 1, 1, 1, 72, 148, 175, 175, 201, 201, 201, 201, 201, 148, 148, 148, 137, 137, 72, 72, 72, 72, 72, 40, 40, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 778 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478220 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478220 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478220/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478220 Building REAL300025478221 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478221' /scratch/stefan/7787258/working/building/REAL300025478221 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478221 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478221/0 /scratch/stefan/7787258/working/building/REAL300025478221 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/78 `/scratch/stefan/7787258/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478221 none C#CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 15, 11, 15, 5, 11, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 53, 53, 53, 53, 53, 1, 25, 25, 25, 25, 25, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478221 none C#CCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 170, 190, 126, 170, 53, 53, 53, 53, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 170, 170, 170, 126, 126, 53, 53, 53, 53, 53, 25, 25, 1, 53, 53] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478221 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478221 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478221/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478221 Building REAL300025478222 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478222' /scratch/stefan/7787258/working/building/REAL300025478222 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478222 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478222/0 /scratch/stefan/7787258/working/building/REAL300025478222 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/79 `/scratch/stefan/7787258/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CCC1) `REAL300025478222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 73, 73, 73, 73, 73, 1, 12, 23, 23, 33, 36, 36, 36, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 73, 1, 1, 33, 33, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 261 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: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 31, 36, 36, 36, 36, 47, 47, 87, 114, 201, 201, 201, 201, 201, 36, 6, 11, 1, 1, 1, 1, 1, 19, 19, 19, 31, 31, 36, 36, 36, 36, 36, 87, 87, 201, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 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, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 547 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: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 143, 73, 73, 73, 73, 51, 40, 51, 13, 1, 1, 1, 1, 1, 1, 1, 73, 169, 191, 191, 201, 201, 201, 201, 169, 169, 169, 143, 143, 73, 73, 73, 73, 73, 40, 40, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 786 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478222 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478222/1 /scratch/stefan/7787258/working/building/REAL300025478222 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/80 `/scratch/stefan/7787258/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CCC1) `REAL300025478222.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 13, 13, 13, 13, 1, 5, 5, 5, 5, 9, 9, 9, 9, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 6, 6, 13, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 8, 9, 9, 9, 9, 10, 10, 15, 15, 17, 17, 17, 17, 17, 9, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 9, 9, 9, 9, 9, 15, 15, 17, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478222 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 13, 13, 13, 13, 13, 12, 13, 11, 1, 1, 1, 1, 1, 1, 1, 13, 16, 16, 16, 16, 17, 17, 17, 17, 16, 16, 16, 15, 15, 13, 13, 13, 13, 13, 12, 12, 1, 13, 13, 16, 16, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478222 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478222 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478222/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478222/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478222 Building REAL300025478223 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478223' /scratch/stefan/7787258/working/building/REAL300025478223 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478223 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478223/0 /scratch/stefan/7787258/working/building/REAL300025478223 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/81 `/scratch/stefan/7787258/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478223 none CC(C)C(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 31, 38, 23, 31, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 86, 86, 86, 86, 86, 1, 38, 38, 38, 38, 38, 38, 38, 31, 93, 23, 23, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 16, 16, 86, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478223 none CC(C)C(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 195, 201, 192, 195, 169, 169, 169, 157, 169, 86, 86, 86, 86, 62, 47, 62, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 195, 585, 192, 192, 169, 169, 169, 157, 157, 86, 86, 86, 86, 86, 47, 47, 1, 86, 86] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478223 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478223 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478223/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478223 Building REAL300025478224 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478224' /scratch/stefan/7787258/working/building/REAL300025478224 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478224 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478224/0 /scratch/stefan/7787258/working/building/REAL300025478224 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/82 `/scratch/stefan/7787258/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CCC1) `REAL300025478224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478224 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 20, 64, 64, 64, 64, 64, 1, 15, 29, 29, 37, 37, 37, 37, 37, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 13, 13, 64, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 216 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: REAL300025478224 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 26, 37, 37, 37, 37, 54, 54, 93, 120, 201, 201, 201, 201, 201, 37, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 37, 37, 37, 37, 37, 93, 93, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 557 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: REAL300025478224 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C(Cl)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 133, 64, 64, 64, 64, 52, 43, 52, 13, 1, 1, 1, 1, 1, 1, 1, 64, 151, 167, 167, 201, 201, 201, 201, 201, 151, 151, 151, 133, 133, 64, 64, 64, 64, 64, 43, 43, 1, 64, 64, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 715 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478224 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478224 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478224/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478224 Building REAL300025478225 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478225' /scratch/stefan/7787258/working/building/REAL300025478225 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478225 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478225/0 /scratch/stefan/7787258/working/building/REAL300025478225 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/83 `/scratch/stefan/7787258/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1) `REAL300025478225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478225 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 23, 34, 34, 34, 34, 47, 47, 85, 111, 201, 201, 201, 201, 201, 34, 1, 1, 2, 2, 2, 1, 1, 12, 12, 12, 23, 23, 34, 34, 34, 34, 34, 85, 85, 201, 34, 34, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478225 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 146, 160, 121, 146, 58, 58, 58, 58, 45, 38, 45, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 146, 146, 146, 121, 121, 58, 58, 58, 58, 58, 38, 38, 1, 58, 58, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 699 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478225 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 24, 13, 24, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 58, 58, 58, 58, 58, 1, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1, 34] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478225 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478225 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478225/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478225 Building REAL300025478226 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478226' /scratch/stefan/7787258/working/building/REAL300025478226 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478226 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478226/0 /scratch/stefan/7787258/working/building/REAL300025478226 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/84 `/scratch/stefan/7787258/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC(=O)NN1) `REAL300025478226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478226 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC(=O)NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 19, 58, 58, 58, 58, 58, 1, 12, 22, 22, 32, 45, 45, 45, 45, 45, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1, 32, 32, 45, 45, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 250 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: REAL300025478226 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC(=O)NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 37, 45, 45, 45, 45, 64, 64, 108, 132, 201, 201, 201, 201, 201, 45, 6, 16, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 37, 37, 45, 45, 45, 45, 45, 108, 108, 201, 45, 45, 6, 6, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 608 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: REAL300025478226 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC(=O)NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 99, 58, 58, 58, 58, 49, 42, 49, 13, 1, 1, 1, 1, 1, 1, 1, 58, 124, 151, 151, 164, 201, 201, 201, 201, 201, 124, 124, 124, 99, 99, 58, 58, 58, 58, 58, 42, 42, 1, 58, 58, 164, 164, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 729 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478226 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478226 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478226/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478226 Building REAL300025478227 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478227' /scratch/stefan/7787258/working/building/REAL300025478227 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478227 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478227/0 /scratch/stefan/7787258/working/building/REAL300025478227 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/85 `/scratch/stefan/7787258/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)CC(C)(C)C) `REAL300025478227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478227 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 69, 69, 69, 69, 69, 1, 15, 27, 27, 36, 36, 40, 40, 40, 40, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 13, 13, 69, 1, 1, 36, 108, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 389 number of broken/clashed sets: 591 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478227 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [160, 134, 69, 69, 69, 69, 49, 39, 49, 12, 1, 1, 1, 1, 1, 1, 1, 69, 160, 190, 190, 201, 201, 201, 201, 201, 201, 160, 160, 160, 134, 134, 69, 69, 69, 69, 69, 39, 39, 1, 69, 69, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 1371 number of broken/clashed sets: 591 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478227 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478227 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478227/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478227 Building REAL300025478228 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478228' /scratch/stefan/7787258/working/building/REAL300025478228 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478228 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478228/0 /scratch/stefan/7787258/working/building/REAL300025478228 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/86 `/scratch/stefan/7787258/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478228 none CCCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 19, 19, 19, 19, 12, 19, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 67, 67, 67, 67, 67, 1, 32, 32, 32, 32, 32, 32, 32, 19, 19, 19, 57, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 67, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 306 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478228 none CCCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 188, 188, 188, 188, 154, 188, 116, 154, 67, 67, 67, 67, 48, 40, 48, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 564, 154, 154, 154, 116, 116, 67, 67, 67, 67, 67, 40, 40, 1, 67, 67] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1356 number of broken/clashed sets: 203 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478228 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478228 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478228/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478228 Building REAL300025478229 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478229' /scratch/stefan/7787258/working/building/REAL300025478229 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478229 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478229/0 /scratch/stefan/7787258/working/building/REAL300025478229 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/87 `/scratch/stefan/7787258/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478229 none CCOC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 20, 20, 20, 20, 12, 20, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 50, 50, 50, 50, 50, 1, 26, 26, 26, 26, 26, 20, 20, 20, 20, 20, 20, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 50, 1, 1] 201 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478229 none CCOC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 195, 195, 195, 136, 195, 111, 136, 50, 50, 50, 50, 35, 29, 35, 11, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 136, 136, 136, 111, 111, 50, 50, 50, 50, 50, 29, 29, 1, 50, 50] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 766 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478229 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478229 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478229/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478229 Building REAL300025478230 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478230' /scratch/stefan/7787258/working/building/REAL300025478230 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478230 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478230/0 /scratch/stefan/7787258/working/building/REAL300025478230 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/88 `/scratch/stefan/7787258/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1) `REAL300025478230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478230 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 4, 4, 11, 21, 21, 21, 21, 40, 40, 69, 107, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 11, 11, 21, 21, 21, 21, 21, 69, 69, 201, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478230 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 130, 130, 114, 130, 59, 59, 59, 59, 43, 37, 43, 12, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 130, 130, 130, 114, 114, 59, 59, 59, 59, 59, 37, 37, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478230 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 59, 59, 59, 59, 59, 1, 21, 21, 21, 21, 21, 21, 21, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 59, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478230 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478230 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478230/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478230 Building REAL300025478231 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478231' /scratch/stefan/7787258/working/building/REAL300025478231 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478231 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478231/0 /scratch/stefan/7787258/working/building/REAL300025478231 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/89 `/scratch/stefan/7787258/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@H+](C)C1) `REAL300025478231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 11, 11, 11, 11, 11, 1, 5, 6, 6, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 4, 4, 11, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 11 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 8, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 11 rigid atoms, others: [43, 44, 45, 46, 47, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50]) total number of confs: 49 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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 10, 11, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 20 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478231 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478231/1 /scratch/stefan/7787258/working/building/REAL300025478231 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/90 `/scratch/stefan/7787258/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@@H+](C)C1) `REAL300025478231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 16, 16, 16, 16, 16, 1, 7, 11, 11, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 5, 5, 16, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 25 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 14, 16, 16, 16, 16, 17, 17, 21, 21, 25, 25, 25, 25, 25, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 14, 14, 16, 16, 16, 16, 16, 21, 21, 25, 16, 16, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [43, 44, 45, 46, 47, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50]) total number of confs: 97 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: REAL300025478231 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C1CC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 16, 16, 16, 16, 16, 16, 16, 11, 1, 1, 1, 1, 1, 1, 1, 16, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 20, 20, 16, 16, 16, 16, 16, 16, 16, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478231 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478231 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478231/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478231/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478231 Building REAL300025478232 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478232' /scratch/stefan/7787258/working/building/REAL300025478232 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478232 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478232/0 /scratch/stefan/7787258/working/building/REAL300025478232 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/91 `/scratch/stefan/7787258/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478232 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 17, 30, 30, 30, 30, 41, 41, 69, 98, 189, 189, 189, 189, 189, 30, 1, 2, 2, 2, 2, 2, 2, 1, 10, 10, 10, 17, 17, 30, 30, 30, 30, 30, 69, 69, 189, 30, 30] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478232 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 187, 189, 136, 187, 65, 65, 65, 65, 46, 36, 46, 13, 1, 1, 1, 1, 1, 1, 1, 65, 189, 189, 189, 189, 189, 189, 189, 189, 187, 187, 187, 136, 136, 65, 65, 65, 65, 65, 36, 36, 1, 65, 65] 189 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 713 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478232 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 20, 15, 20, 7, 15, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 65, 65, 65, 65, 65, 1, 30, 30, 30, 30, 30, 30, 30, 30, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 11, 11, 65, 1, 1] 189 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478232 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478232 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478232/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478232 Building REAL300025478233 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478233' /scratch/stefan/7787258/working/building/REAL300025478233 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478233 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478233/0 /scratch/stefan/7787258/working/building/REAL300025478233 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/92 `/scratch/stefan/7787258/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478233 none CCOC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 3, 3, 5, 5, 13, 23, 23, 23, 23, 38, 38, 71, 102, 201, 201, 201, 201, 201, 23, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 71, 71, 201, 23, 23, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478233 none CCOC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 125, 139, 106, 125, 52, 52, 52, 52, 39, 32, 39, 11, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 106, 106, 52, 52, 52, 52, 52, 32, 32, 1, 52, 52, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 775 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478233 none CCOC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 23, 15, 9, 15, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 52, 52, 52, 52, 52, 1, 23, 23, 23, 25, 25, 25, 25, 25, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 52, 1, 1, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478233 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478233 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478233/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478233 Building REAL300025478234 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478234' /scratch/stefan/7787258/working/building/REAL300025478234 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478234 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478234/0 /scratch/stefan/7787258/working/building/REAL300025478234 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/93 `/scratch/stefan/7787258/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478234 none C#C[C@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 22, 22, 22, 22, 40, 40, 78, 111, 201, 201, 201, 201, 201, 22, 1, 1, 1, 6, 6, 6, 13, 13, 22, 22, 22, 22, 22, 78, 78, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 520 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: REAL300025478234 none C#C[C@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 197, 201, 166, 197, 85, 85, 85, 85, 52, 39, 52, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 197, 197, 197, 166, 166, 85, 85, 85, 85, 85, 39, 39, 1, 85, 85] 201 rigid atoms, others: [42, 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, 43, 44]) total number of confs: 750 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: REAL300025478234 none C#C[C@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 18, 22, 14, 18, 6, 14, 1, 1, 1, 1, 1, 1, 6, 6, 17, 27, 85, 85, 85, 85, 85, 1, 22, 22, 22, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 17, 17, 85, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 44, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 226 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478234 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478234 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478234/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478234 Building REAL300025478235 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478235' /scratch/stefan/7787258/working/building/REAL300025478235 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478235 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478235/0 /scratch/stefan/7787258/working/building/REAL300025478235 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/94 `/scratch/stefan/7787258/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(=O)[N-]1) `REAL300025478235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478235 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 2, 2, 10, 18, 76, 76, 76, 76, 76, 1, 12, 19, 19, 37, 37, 37, 37, 37, 37, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 76, 1, 1, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478235 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 24, 37, 37, 37, 37, 42, 42, 81, 109, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 37, 37, 37, 37, 37, 81, 81, 201, 37, 37, 2, 2, 2] 201 rigid atoms, others: [18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478235 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 138, 76, 76, 76, 76, 54, 47, 54, 13, 1, 1, 1, 1, 1, 1, 1, 76, 157, 167, 167, 201, 201, 201, 201, 201, 201, 157, 157, 157, 138, 138, 76, 76, 76, 76, 76, 47, 47, 1, 76, 76, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478235 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478235 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478235/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478235 Building REAL300025478236 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478236' /scratch/stefan/7787258/working/building/REAL300025478236 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478236 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478236/0 /scratch/stefan/7787258/working/building/REAL300025478236 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/95 `/scratch/stefan/7787258/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(N=[N+]=[N-])CC1) `REAL300025478236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478236 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(N=[N+]=[N-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 8, 8, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 22, 59, 59, 59, 59, 59, 1, 11, 20, 20, 26, 34, 34, 26, 26, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 59, 1, 1, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478236 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(N=[N+]=[N-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 8, 8, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 18, 26, 26, 26, 26, 44, 44, 79, 114, 201, 201, 201, 201, 201, 26, 1, 6, 1, 1, 6, 6, 1, 1, 10, 10, 10, 18, 18, 26, 26, 26, 26, 26, 79, 79, 201, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 18, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 517 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478236 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(N=[N+]=[N-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 8, 8, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 133, 59, 59, 59, 59, 46, 37, 46, 12, 1, 1, 1, 1, 1, 1, 1, 59, 147, 178, 178, 201, 201, 201, 201, 201, 147, 147, 147, 133, 133, 59, 59, 59, 59, 59, 37, 37, 1, 59, 59, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478236 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478236 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478236/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478236 Building REAL300025478237 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478237' /scratch/stefan/7787258/working/building/REAL300025478237 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478237 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478237/0 /scratch/stefan/7787258/working/building/REAL300025478237 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/96 `/scratch/stefan/7787258/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(=O)O1) `REAL300025478237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478237 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 20, 66, 66, 66, 66, 66, 1, 14, 33, 33, 39, 39, 39, 39, 39, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 66, 1, 1, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478237 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 28, 39, 39, 39, 39, 55, 55, 97, 124, 201, 201, 201, 201, 201, 39, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 28, 39, 39, 39, 39, 39, 97, 97, 201, 39, 39, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 587 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478237 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 130, 66, 66, 66, 66, 51, 38, 51, 13, 1, 1, 1, 1, 1, 1, 1, 66, 157, 200, 200, 201, 201, 201, 201, 201, 157, 157, 157, 130, 130, 66, 66, 66, 66, 66, 38, 38, 1, 66, 66, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478237 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478237 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478237/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478237 Building REAL300025478238 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478238' /scratch/stefan/7787258/working/building/REAL300025478238 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478238 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478238/0 /scratch/stefan/7787258/working/building/REAL300025478238 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/97 `/scratch/stefan/7787258/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478238 none CC(C)[C@@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 16, 27, 27, 27, 27, 43, 43, 84, 109, 201, 201, 201, 201, 201, 27, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 7, 16, 16, 27, 27, 27, 27, 27, 84, 84, 201, 27, 27] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 36] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478238 none CC(C)[C@@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 162, 201, 161, 162, 137, 161, 65, 65, 65, 65, 44, 38, 44, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 161, 161, 137, 137, 65, 65, 65, 65, 65, 38, 38, 1, 65, 65] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 764 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478238 none CC(C)[C@@H]1C[C@H]1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 27, 27, 27, 15, 27, 14, 15, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 65, 65, 65, 65, 65, 1, 35, 35, 35, 35, 35, 35, 35, 27, 27, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 64, 1, 1] 201 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 50, 51, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478238 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478238 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478238/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478238 Building REAL300025478239 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478239' /scratch/stefan/7787258/working/building/REAL300025478239 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478239 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478239/0 /scratch/stefan/7787258/working/building/REAL300025478239 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/98 `/scratch/stefan/7787258/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(Cl)=N1) `REAL300025478239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 21, 64, 64, 64, 64, 64, 1, 15, 30, 30, 35, 35, 35, 35, 35, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 13, 13, 64, 1, 1, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 25, 35, 35, 35, 35, 51, 51, 82, 111, 201, 201, 201, 201, 201, 35, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 25, 25, 35, 35, 35, 35, 35, 82, 82, 201, 35, 35, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 128, 64, 64, 64, 64, 48, 43, 48, 13, 1, 1, 1, 1, 1, 1, 1, 64, 174, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 128, 128, 64, 64, 64, 64, 64, 43, 43, 1, 64, 64, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478239 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478239/1 /scratch/stefan/7787258/working/building/REAL300025478239 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/99 `/scratch/stefan/7787258/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=C(Cl)N1) `REAL300025478239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 14, 37, 37, 37, 37, 37, 1, 10, 19, 19, 27, 27, 27, 27, 27, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 37, 1, 1, 27, 27] 63 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 147 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: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 16, 23, 27, 27, 27, 27, 32, 32, 42, 49, 63, 63, 63, 63, 63, 27, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 27, 27, 27, 27, 27, 42, 42, 63, 27, 27, 1, 1] 63 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 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: REAL300025478239 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=C(Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 16, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 53, 37, 37, 37, 37, 35, 33, 35, 13, 1, 1, 1, 1, 1, 1, 1, 37, 59, 62, 62, 63, 63, 63, 63, 63, 59, 59, 59, 53, 53, 37, 37, 37, 37, 37, 33, 33, 1, 37, 37, 63, 63] 63 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 239 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478239 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478239 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478239/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478239/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478239 Building REAL300025478240 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478240' /scratch/stefan/7787258/working/building/REAL300025478240 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478240 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478240/0 /scratch/stefan/7787258/working/building/REAL300025478240 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/100 `/scratch/stefan/7787258/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC2CCCC12) `REAL300025478240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478240 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC2CCCC12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 50, 50, 50, 50, 50, 1, 15, 28, 28, 43, 43, 43, 43, 43, 43, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 50, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 200 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: REAL300025478240 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC2CCCC12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 30, 43, 43, 43, 43, 53, 53, 96, 121, 201, 201, 201, 201, 201, 43, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 30, 30, 43, 43, 43, 43, 43, 96, 96, 201, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 579 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: REAL300025478240 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC2CCCC12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 105, 50, 50, 50, 50, 39, 32, 39, 12, 1, 1, 1, 1, 1, 1, 1, 50, 129, 173, 173, 201, 201, 201, 201, 201, 201, 129, 129, 129, 105, 105, 50, 50, 50, 50, 50, 32, 32, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 720 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478240 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478240 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478240/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478240 Building REAL300025478241 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478241' /scratch/stefan/7787258/working/building/REAL300025478241 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478241 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478241/0 /scratch/stefan/7787258/working/building/REAL300025478241 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/101 `/scratch/stefan/7787258/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CN=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478241 none CCN1N=CN=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 19, 19, 19, 19, 29, 29, 57, 76, 153, 153, 153, 153, 153, 19, 5, 5, 5, 4, 4, 1, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 57, 57, 153, 19, 19] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478241 none CCN1N=CN=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 153, 153, 153, 153, 135, 135, 135, 106, 135, 58, 58, 58, 58, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 153, 135, 135, 135, 106, 106, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58] 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, 46, 47]) total number of confs: 838 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478241 none CCN1N=CN=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 19, 19, 19, 19, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 58, 58, 58, 58, 58, 1, 35, 35, 35, 35, 35, 19, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 10, 10, 58, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 46, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478241 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478241 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478241/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478241 Building REAL300025478242 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478242' /scratch/stefan/7787258/working/building/REAL300025478242 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478242 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478242/0 /scratch/stefan/7787258/working/building/REAL300025478242 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/102 `/scratch/stefan/7787258/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478242 none CC(C)C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 8, 8, 18, 32, 32, 32, 32, 45, 45, 85, 111, 201, 201, 201, 201, 201, 32, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 8, 18, 18, 32, 32, 32, 32, 32, 85, 85, 201, 32, 32, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 53, 54, 36, 26, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478242 none CC(C)C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 123, 126, 104, 123, 56, 56, 56, 56, 44, 34, 44, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 104, 104, 56, 56, 56, 56, 56, 34, 34, 1, 56, 56, 201, 201] 201 rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 765 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478242 none CC(C)C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 32, 39, 32, 32, 15, 13, 15, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 56, 56, 56, 56, 56, 1, 32, 39, 39, 39, 39, 39, 39, 39, 32, 32, 32, 32, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 12, 12, 56, 1, 1, 32, 32] 201 rigid atoms, others: [43, 15, 44, 10, 11, 12, 13, 14, 45, 51, 52, 46, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478242 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478242 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478242/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478242 Building REAL300025478243 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478243' /scratch/stefan/7787258/working/building/REAL300025478243 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478243 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478243/0 /scratch/stefan/7787258/working/building/REAL300025478243 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/103 `/scratch/stefan/7787258/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCOC1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478243 none CC1CCOC1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 22, 36, 36, 36, 36, 55, 55, 95, 120, 201, 201, 201, 201, 201, 36, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 22, 22, 36, 36, 36, 36, 36, 95, 95, 201, 36, 36] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478243 none CC1CCOC1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 188, 181, 188, 151, 181, 78, 78, 78, 78, 52, 40, 52, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 151, 151, 78, 78, 78, 78, 78, 40, 40, 1, 78, 78] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 764 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478243 none CC1CCOC1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 18, 15, 18, 6, 15, 1, 1, 1, 1, 1, 1, 6, 6, 13, 22, 78, 78, 78, 78, 78, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 13, 13, 78, 1, 1] 201 rigid atoms, others: [11, 47, 44, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478243 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478243 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478243/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478243 Building REAL300025478244 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478244' /scratch/stefan/7787258/working/building/REAL300025478244 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478244 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478244/0 /scratch/stefan/7787258/working/building/REAL300025478244 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/104 `/scratch/stefan/7787258/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H](N=[N+]=[N-])C1) `REAL300025478244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478244 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H](N=[N+]=[N-])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 64, 64, 64, 64, 64, 1, 10, 16, 16, 21, 21, 21, 21, 21, 47, 47, 21, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 64, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478244 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H](N=[N+]=[N-])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 15, 21, 21, 21, 21, 31, 31, 54, 73, 163, 163, 163, 163, 163, 21, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 1, 7, 7, 7, 15, 15, 21, 21, 21, 21, 21, 54, 54, 163, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478244 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H](N=[N+]=[N-])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 8, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 108, 64, 64, 64, 64, 47, 38, 47, 13, 1, 1, 1, 1, 1, 1, 1, 64, 120, 138, 138, 163, 163, 163, 163, 163, 201, 201, 163, 120, 120, 120, 108, 108, 64, 64, 64, 64, 64, 38, 38, 1, 64, 64, 163, 163, 163, 163] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478244 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478244 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478244/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478244 Building REAL300025478245 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478245' /scratch/stefan/7787258/working/building/REAL300025478245 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478245 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478245/0 /scratch/stefan/7787258/working/building/REAL300025478245 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/105 `/scratch/stefan/7787258/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CO1)C2) `REAL300025478245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478245 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CO1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 21, 72, 72, 72, 72, 72, 1, 12, 21, 21, 26, 26, 26, 26, 26, 26, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 72, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478245 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CO1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 21, 26, 26, 26, 26, 38, 38, 72, 105, 201, 201, 201, 201, 201, 26, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 26, 26, 26, 26, 26, 72, 72, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 530 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478245 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CO1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 146, 72, 72, 72, 72, 50, 41, 50, 13, 1, 1, 1, 1, 1, 1, 1, 72, 179, 199, 199, 201, 201, 201, 201, 201, 201, 179, 179, 179, 146, 146, 72, 72, 72, 72, 72, 41, 41, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 776 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478245 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478245 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478245/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478245 Building REAL300025478246 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478246' /scratch/stefan/7787258/working/building/REAL300025478246 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478246 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478246/0 /scratch/stefan/7787258/working/building/REAL300025478246 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/106 `/scratch/stefan/7787258/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCC21) `REAL300025478246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478246 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 47, 47, 47, 47, 47, 1, 11, 17, 17, 28, 28, 28, 28, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 47, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478246 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 21, 28, 28, 28, 28, 47, 47, 87, 114, 201, 201, 201, 201, 201, 28, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 28, 28, 28, 28, 28, 87, 87, 201, 28, 28, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478246 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 107, 47, 47, 47, 47, 35, 31, 35, 13, 1, 1, 1, 1, 1, 1, 1, 47, 127, 137, 137, 201, 201, 201, 201, 127, 127, 127, 107, 107, 47, 47, 47, 47, 47, 31, 31, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478246 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478246 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478246/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478246 Building REAL300025478247 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478247' /scratch/stefan/7787258/working/building/REAL300025478247 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478247 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478247/0 /scratch/stefan/7787258/working/building/REAL300025478247 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/107 `/scratch/stefan/7787258/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478247 none C=C1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 16, 26, 26, 26, 26, 46, 46, 86, 118, 201, 201, 201, 201, 201, 26, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 26, 26, 26, 26, 26, 86, 86, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478247 none C=C1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 174, 172, 174, 151, 172, 72, 72, 72, 72, 49, 37, 49, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 151, 151, 72, 72, 72, 72, 72, 37, 37, 1, 72, 72] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 774 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478247 none C=C1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 14, 12, 14, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 72, 72, 72, 72, 72, 1, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 14, 14, 72, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478247 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478247 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478247/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478247 Building REAL300025478248 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478248' /scratch/stefan/7787258/working/building/REAL300025478248 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478248 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478248/0 /scratch/stefan/7787258/working/building/REAL300025478248 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/108 `/scratch/stefan/7787258/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)[C@H]1C) `REAL300025478248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478248 none C[C@H]1C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 5, 5, 10, 16, 16, 16, 16, 36, 36, 71, 106, 201, 201, 201, 201, 201, 16, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 10, 10, 16, 16, 16, 16, 16, 71, 71, 201, 16, 16, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 512 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478248 none C[C@H]1C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 190, 201, 166, 190, 77, 77, 77, 77, 52, 41, 52, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 166, 166, 77, 77, 77, 77, 77, 41, 41, 1, 77, 77, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 759 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: REAL300025478248 none C[C@H]1C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 12, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 77, 77, 77, 77, 77, 1, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 16, 16, 77, 1, 1, 16, 16, 16] 201 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478248 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478248 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478248/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478248 Building REAL300025478249 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478249' /scratch/stefan/7787258/working/building/REAL300025478249 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478249 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478249/0 /scratch/stefan/7787258/working/building/REAL300025478249 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/109 `/scratch/stefan/7787258/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478249 none C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 6, 7, 3, 6, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 16, 16, 16, 16, 16, 1, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 5, 5, 16, 1, 1, 9, 9, 9, 9, 9, 9] 20 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478249 none C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 16, 20, 16, 16, 16, 16, 16, 15, 16, 12, 1, 1, 1, 1, 1, 1, 1, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 16, 15, 15, 1, 16, 16, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 51 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478249 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478249/1 /scratch/stefan/7787258/working/building/REAL300025478249 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/110 `/scratch/stefan/7787258/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C) `REAL300025478249.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478249 none C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 36, 15, 19, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 84, 84, 84, 84, 84, 1, 36, 41, 41, 36, 36, 36, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 16, 16, 84, 1, 1, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478249 none C[C@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 201, 177, 185, 153, 177, 84, 84, 84, 84, 58, 42, 58, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 177, 177, 177, 153, 153, 84, 84, 84, 84, 84, 42, 42, 1, 84, 84, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478249 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478249 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478249/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478249/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478249 Building REAL300025478250 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478250' /scratch/stefan/7787258/working/building/REAL300025478250 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478250 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478250/0 /scratch/stefan/7787258/working/building/REAL300025478250 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/111 `/scratch/stefan/7787258/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CN=CN1) `REAL300025478250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 79, 79, 79, 79, 79, 1, 12, 22, 22, 41, 41, 51, 51, 51, 51, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 16, 16, 79, 1, 1, 41, 123, 51, 51, 51] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 456 number of broken/clashed sets: 213 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 20, 30, 47, 51, 51, 51, 51, 72, 72, 116, 139, 201, 201, 201, 201, 201, 51, 9, 20, 1, 9, 1, 1, 1, 1, 1, 30, 30, 30, 47, 47, 51, 51, 51, 51, 51, 116, 116, 201, 51, 51, 9, 27, 1, 1, 1] 603 rigid atoms, others: [44, 45, 46, 20, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 646 number of broken/clashed sets: 213 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [148, 131, 79, 79, 79, 79, 57, 46, 57, 13, 1, 1, 1, 1, 1, 1, 1, 79, 148, 176, 176, 198, 198, 201, 201, 201, 201, 148, 148, 148, 131, 131, 79, 79, 79, 79, 79, 46, 46, 1, 79, 79, 198, 594, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1393 number of broken/clashed sets: 213 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478250 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478250/1 /scratch/stefan/7787258/working/building/REAL300025478250 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/112 `/scratch/stefan/7787258/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CNC=N1) `REAL300025478250.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 14, 25, 94, 94, 94, 94, 94, 1, 16, 28, 28, 29, 29, 41, 41, 41, 41, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 14, 14, 94, 1, 1, 29, 87, 41, 41, 41] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 349 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 9, 14, 26, 41, 41, 41, 41, 55, 55, 90, 117, 201, 201, 201, 201, 201, 41, 6, 9, 1, 6, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 41, 41, 41, 41, 41, 90, 90, 201, 41, 41, 6, 18, 1, 1, 1] 603 rigid atoms, others: [44, 45, 46, 20, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 581 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478250 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [188, 156, 94, 94, 94, 94, 69, 57, 69, 13, 1, 1, 1, 1, 1, 1, 1, 94, 188, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 156, 156, 94, 94, 94, 94, 94, 57, 57, 1, 94, 94, 201, 603, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1350 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478250 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478250 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478250/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478250/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478250 Building REAL300025478251 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478251' /scratch/stefan/7787258/working/building/REAL300025478251 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478251 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478251/0 /scratch/stefan/7787258/working/building/REAL300025478251 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/113 `/scratch/stefan/7787258/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478251 none CCC(C)(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 37, 11, 37, 37, 11, 11, 9, 11, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 9, 13, 50, 50, 50, 50, 50, 1, 44, 44, 44, 44, 44, 37, 37, 37, 37, 37, 37, 11, 33, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 9, 9, 50, 1, 1] 603 rigid atoms, others: [16, 15, 11, 12, 13, 14, 45, 48, 49, 46, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52]) total number of confs: 302 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478251 none CCC(C)(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 104, 201, 201, 104, 104, 92, 104, 81, 92, 50, 50, 50, 50, 49, 41, 49, 13, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 312, 92, 92, 92, 81, 81, 50, 50, 50, 50, 50, 41, 41, 1, 50, 50] 603 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 1190 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478251 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478251 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478251/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478251 Building REAL300025478252 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478252' /scratch/stefan/7787258/working/building/REAL300025478252 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478252 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478252/0 /scratch/stefan/7787258/working/building/REAL300025478252 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/114 `/scratch/stefan/7787258/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478252 none CC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 47, 47, 18, 16, 18, 6, 16, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 78, 78, 78, 78, 78, 1, 48, 48, 48, 48, 48, 47, 47, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 16, 16, 78, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 268 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: REAL300025478252 none CC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 174, 175, 161, 174, 78, 78, 78, 78, 58, 44, 58, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 161, 161, 78, 78, 78, 78, 78, 44, 44, 1, 78, 78] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 768 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478252 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478252 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478252/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478252 Building REAL300025478253 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478253' /scratch/stefan/7787258/working/building/REAL300025478253 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478253 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478253/0 /scratch/stefan/7787258/working/building/REAL300025478253 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/115 `/scratch/stefan/7787258/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=NN1C) `REAL300025478253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478253 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 58, 58, 58, 58, 58, 1, 11, 25, 25, 27, 27, 27, 27, 27, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478253 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 20, 27, 27, 27, 27, 43, 43, 82, 111, 201, 201, 201, 201, 201, 27, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 27, 27, 27, 27, 27, 82, 82, 201, 27, 27, 1, 2, 2, 2] 201 rigid atoms, others: [41, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478253 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 121, 58, 58, 58, 58, 43, 37, 43, 12, 1, 1, 1, 1, 1, 1, 1, 58, 145, 200, 200, 201, 201, 201, 201, 201, 145, 145, 145, 121, 121, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478253 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478253 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478253/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478253 Building REAL300025478254 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478254' /scratch/stefan/7787258/working/building/REAL300025478254 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478254 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478254/0 /scratch/stefan/7787258/working/building/REAL300025478254 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/116 `/scratch/stefan/7787258/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC[C@@H](O)C1) `REAL300025478254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478254 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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: [15, 5, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 69, 69, 69, 69, 69, 1, 15, 27, 27, 42, 42, 42, 42, 42, 42, 42, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 14, 14, 69, 1, 1, 42, 42, 42, 42, 126, 42, 42] 603 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 381 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: REAL300025478254 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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: [18, 6, 18, 32, 42, 42, 42, 42, 51, 51, 92, 115, 201, 201, 201, 201, 201, 42, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 32, 32, 42, 42, 42, 42, 42, 92, 92, 201, 42, 42, 1, 1, 1, 1, 6, 1, 1] 603 rigid atoms, others: [43, 44, 45, 46, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47]) total number of confs: 568 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: REAL300025478254 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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: [153, 134, 69, 69, 69, 69, 49, 38, 49, 13, 1, 1, 1, 1, 1, 1, 1, 69, 153, 185, 185, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 134, 134, 69, 69, 69, 69, 69, 38, 38, 1, 69, 69, 201, 201, 201, 201, 603, 201, 201] 603 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1393 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478254 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478254 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478254/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478254 Building REAL300025478255 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478255' /scratch/stefan/7787258/working/building/REAL300025478255 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478255 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478255/0 /scratch/stefan/7787258/working/building/REAL300025478255 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/117 `/scratch/stefan/7787258/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CS(C)=O) `REAL300025478255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478255 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CS(C)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 14, 5, 11, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 74, 74, 74, 74, 74, 1, 11, 22, 22, 29, 29, 41, 41, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 74, 1, 1, 29, 29, 41, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 262 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478255 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CS(C)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 14, 5, 11, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 129, 74, 74, 74, 74, 59, 48, 59, 13, 1, 1, 1, 1, 1, 1, 1, 74, 157, 187, 187, 201, 201, 201, 201, 157, 157, 157, 129, 129, 74, 74, 74, 74, 74, 48, 48, 1, 74, 74, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 752 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478255 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478255 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478255/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478255 Building REAL300025478256 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478256' /scratch/stefan/7787258/working/building/REAL300025478256 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478256 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478256/0 /scratch/stefan/7787258/working/building/REAL300025478256 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/118 `/scratch/stefan/7787258/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC=CCC1) `REAL300025478256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478256 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 6, 7, 14, 23, 61, 61, 61, 61, 61, 1, 10, 21, 21, 28, 28, 28, 28, 28, 28, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 14, 14, 61, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 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: REAL300025478256 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 24, 28, 28, 28, 28, 37, 37, 74, 103, 201, 201, 201, 201, 201, 28, 1, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 28, 28, 28, 28, 28, 74, 74, 201, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 524 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: REAL300025478256 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 128, 61, 61, 61, 61, 42, 33, 42, 11, 1, 1, 1, 1, 1, 1, 1, 61, 148, 183, 183, 201, 201, 201, 201, 201, 201, 148, 148, 148, 128, 128, 61, 61, 61, 61, 61, 33, 33, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 771 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478256 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478256 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478256/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478256 Building REAL300025478257 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478257' /scratch/stefan/7787258/working/building/REAL300025478257 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478257 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478257/0 /scratch/stefan/7787258/working/building/REAL300025478257 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/119 `/scratch/stefan/7787258/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478257 none COCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 36, 23, 23, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 79, 79, 79, 79, 79, 1, 39, 39, 39, 36, 36, 23, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 79, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 260 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: REAL300025478257 none COCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 189, 165, 165, 165, 147, 165, 79, 79, 79, 79, 55, 44, 55, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 189, 189, 165, 165, 165, 147, 147, 79, 79, 79, 79, 79, 44, 44, 1, 79, 79] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 754 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478257 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478257 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478257/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478257 Building REAL300025478258 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478258' /scratch/stefan/7787258/working/building/REAL300025478258 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478258 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478258/0 /scratch/stefan/7787258/working/building/REAL300025478258 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/120 `/scratch/stefan/7787258/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCOC1COC1) `REAL300025478258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478258 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCOC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 32, 32, 32, 32, 32, 1, 11, 14, 14, 14, 14, 19, 33, 33, 33, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 32, 1, 1, 14, 14, 14, 14, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478258 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCOC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 8, 10, 22, 33, 33, 33, 33, 43, 43, 68, 110, 201, 201, 201, 201, 201, 33, 8, 8, 8, 5, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 33, 33, 33, 33, 33, 68, 68, 201, 33, 33, 8, 8, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478258 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCOC1COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 74, 32, 32, 32, 32, 22, 19, 22, 10, 1, 1, 1, 1, 1, 1, 1, 32, 97, 117, 117, 117, 117, 118, 201, 201, 201, 97, 97, 97, 74, 74, 32, 32, 32, 32, 32, 19, 19, 1, 32, 32, 117, 117, 117, 117, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478258 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478258 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478258/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478258 Building REAL300025478259 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478259' /scratch/stefan/7787258/working/building/REAL300025478259 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478259 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478259/0 /scratch/stefan/7787258/working/building/REAL300025478259 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/121 `/scratch/stefan/7787258/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478259 none CC(=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 24, 11, 13, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 49, 49, 49, 49, 49, 1, 24, 43, 43, 24, 24, 24, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 49, 1, 1, 43, 43, 43, 43, 43] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478259 none CC(=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 4, 11, 11, 13, 13, 28, 43, 43, 43, 43, 57, 57, 89, 115, 201, 201, 201, 201, 201, 43, 1, 1, 1, 4, 4, 4, 13, 13, 13, 28, 28, 43, 43, 43, 43, 43, 89, 89, 201, 43, 43, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478259 none CC(=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 102, 131, 101, 102, 88, 101, 49, 49, 49, 49, 36, 31, 36, 12, 1, 1, 1, 1, 1, 1, 1, 49, 131, 201, 201, 131, 131, 131, 101, 101, 101, 88, 88, 49, 49, 49, 49, 49, 31, 31, 1, 49, 49, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478259 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478259 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478259/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478259 Building REAL300025478260 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478260' /scratch/stefan/7787258/working/building/REAL300025478260 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478260 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478260/0 /scratch/stefan/7787258/working/building/REAL300025478260 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/122 `/scratch/stefan/7787258/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCS(C)=O) `REAL300025478260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478260 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCS(C)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 14, 5, 11, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 52, 52, 52, 52, 52, 1, 11, 17, 17, 17, 17, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 52, 1, 1, 17, 17, 17, 17, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478260 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCS(C)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 14, 5, 11, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 114, 52, 52, 52, 52, 38, 27, 38, 13, 1, 1, 1, 1, 1, 1, 1, 52, 145, 181, 181, 181, 181, 201, 201, 145, 145, 145, 114, 114, 52, 52, 52, 52, 52, 27, 27, 1, 52, 52, 181, 181, 181, 181, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478260 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478260 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478260/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478260 Building REAL300025478261 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478261' /scratch/stefan/7787258/working/building/REAL300025478261 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478261 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478261/0 /scratch/stefan/7787258/working/building/REAL300025478261 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/123 `/scratch/stefan/7787258/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(F)=C1) `REAL300025478261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478261 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 72, 72, 72, 72, 72, 1, 17, 25, 25, 30, 30, 30, 30, 30, 30, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 10, 10, 72, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478261 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 21, 30, 30, 30, 30, 38, 38, 83, 114, 201, 201, 201, 201, 201, 30, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 30, 30, 30, 30, 30, 83, 83, 201, 30, 30, 2, 2, 2, 1] 201 rigid atoms, others: [45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478261 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN(C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 5, 1, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 72, 72, 72, 72, 54, 39, 54, 13, 1, 1, 1, 1, 1, 1, 1, 72, 175, 199, 199, 201, 201, 201, 201, 201, 201, 175, 175, 175, 135, 135, 72, 72, 72, 72, 72, 39, 39, 1, 72, 72, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478261 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478261 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478261/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478261 Building REAL300025478262 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478262' /scratch/stefan/7787258/working/building/REAL300025478262 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478262 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478262/0 /scratch/stefan/7787258/working/building/REAL300025478262 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/124 `/scratch/stefan/7787258/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C(Cl)Cl) `REAL300025478262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478262 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C(Cl)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 42, 42, 42, 42, 42, 1, 9, 13, 13, 30, 30, 30, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39]) total number of confs: 170 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: REAL300025478262 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=C(Cl)Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 80, 42, 42, 42, 42, 28, 24, 28, 12, 1, 1, 1, 1, 1, 1, 1, 42, 100, 134, 134, 201, 201, 201, 100, 100, 100, 80, 80, 42, 42, 42, 42, 42, 24, 24, 1, 42, 42, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 763 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478262 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478262 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478262/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478262 Building REAL300025478263 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478263' /scratch/stefan/7787258/working/building/REAL300025478263 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478263 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478263/0 /scratch/stefan/7787258/working/building/REAL300025478263 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/125 `/scratch/stefan/7787258/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C[N-]N=CC1=O) `REAL300025478263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478263 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C[N-]N=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 8, 1, 1, 11, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 61, 61, 61, 61, 61, 1, 15, 32, 32, 47, 47, 47, 47, 47, 47, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 10, 10, 61, 1, 1, 47, 47] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478263 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C[N-]N=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 8, 1, 1, 11, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 35, 47, 47, 47, 47, 55, 55, 93, 114, 201, 201, 201, 201, 201, 47, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 47, 47, 47, 47, 47, 93, 93, 201, 47, 47, 1, 1] 201 rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 579 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478263 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=C[N-]N=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 8, 1, 1, 11, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 105, 61, 61, 61, 61, 45, 38, 45, 13, 1, 1, 1, 1, 1, 1, 1, 61, 125, 157, 157, 201, 201, 201, 201, 201, 201, 125, 125, 125, 105, 105, 61, 61, 61, 61, 61, 38, 38, 1, 61, 61, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478263 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478263 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478263/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478263 Building REAL300025478264 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478264' /scratch/stefan/7787258/working/building/REAL300025478264 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478264 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478264/0 /scratch/stefan/7787258/working/building/REAL300025478264 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/126 `/scratch/stefan/7787258/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478264 none COC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 28, 45, 45, 45, 45, 67, 67, 115, 139, 201, 201, 201, 201, 201, 45, 1, 2, 2, 2, 1, 14, 14, 14, 28, 28, 45, 45, 45, 45, 45, 115, 115, 201, 45, 45, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 626 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: REAL300025478264 none COC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 143, 160, 114, 143, 59, 59, 59, 59, 49, 40, 49, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 143, 143, 143, 114, 114, 59, 59, 59, 59, 59, 40, 40, 1, 59, 59, 201] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 702 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: REAL300025478264 none COC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 22, 13, 22, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 59, 59, 59, 59, 59, 1, 45, 45, 45, 45, 45, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 12, 12, 59, 1, 1, 45] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46]) total number of confs: 205 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478264 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478264 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478264/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478264 Building REAL300025478265 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478265' /scratch/stefan/7787258/working/building/REAL300025478265 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478265 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478265/0 /scratch/stefan/7787258/working/building/REAL300025478265 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/127 `/scratch/stefan/7787258/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478265 none CC1CN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 12, 14, 14, 26, 39, 39, 39, 39, 53, 53, 86, 114, 201, 201, 201, 201, 201, 39, 1, 2, 2, 2, 1, 1, 1, 5, 5, 14, 14, 14, 26, 26, 39, 39, 39, 39, 39, 86, 86, 201, 39, 39, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 49, 50, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478265 none CC1CN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 149, 155, 126, 149, 61, 61, 61, 61, 44, 34, 44, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 126, 126, 61, 61, 61, 61, 61, 34, 34, 1, 61, 61, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 868 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478265 none CC1CN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 32, 15, 13, 15, 5, 13, 1, 1, 1, 1, 1, 1, 6, 6, 12, 21, 61, 61, 61, 61, 61, 1, 39, 39, 39, 39, 39, 39, 39, 32, 32, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 61, 1, 1, 39, 39] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478265 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478265/1 /scratch/stefan/7787258/working/building/REAL300025478265 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/128 `/scratch/stefan/7787258/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[NH+](CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478265.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478265 none CC1C[NH+](CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 10, 11, 11, 11, 11, 12, 12, 17, 17, 20, 20, 20, 20, 20, 11, 1, 2, 2, 2, 1, 1, 1, 6, 6, 8, 8, 8, 10, 10, 11, 11, 11, 11, 11, 17, 17, 20, 11, 11, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 50, 51, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478265 none CC1C[NH+](CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 19, 20, 16, 16, 16, 15, 16, 13, 13, 13, 13, 13, 13, 13, 11, 1, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 20, 20, 20, 20, 19, 19, 16, 16, 16, 15, 15, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13, 20, 20] 20 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478265 none CC1C[NH+](CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 11, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 13, 13, 1, 11, 11, 11, 11, 11, 11, 11, 6, 6, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 5, 5, 13, 1, 1, 11, 11] 20 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478265 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478265 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478265/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478265/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478265 Building REAL300025478266 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478266' /scratch/stefan/7787258/working/building/REAL300025478266 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478266 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478266/0 /scratch/stefan/7787258/working/building/REAL300025478266 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/129 `/scratch/stefan/7787258/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CCCC1) `REAL300025478266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478266 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 62, 62, 62, 62, 62, 1, 11, 23, 23, 28, 28, 38, 38, 38, 38, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 15, 62, 1, 1, 28, 84, 38, 38, 38, 38, 38, 38, 38, 38, 38] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 341 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478266 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [17, 10, 17, 29, 38, 38, 38, 38, 52, 52, 102, 130, 201, 201, 201, 201, 201, 38, 4, 10, 1, 4, 1, 1, 1, 1, 1, 17, 17, 17, 29, 29, 38, 38, 38, 38, 38, 102, 102, 201, 38, 38, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 162 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478266 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [126, 110, 62, 62, 62, 62, 45, 38, 45, 12, 1, 1, 1, 1, 1, 1, 1, 62, 126, 169, 169, 175, 175, 201, 201, 201, 201, 126, 126, 126, 110, 110, 62, 62, 62, 62, 62, 38, 38, 1, 62, 62, 175, 525, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1313 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478266 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478266 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478266/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478266 Building REAL300025478267 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478267' /scratch/stefan/7787258/working/building/REAL300025478267 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478267 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478267/0 /scratch/stefan/7787258/working/building/REAL300025478267 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/130 `/scratch/stefan/7787258/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)COC1) `REAL300025478267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478267 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 14, 50, 50, 50, 50, 50, 1, 10, 19, 19, 19, 19, 19, 19, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 9, 9, 50, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 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: REAL300025478267 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 13, 19, 19, 19, 19, 29, 29, 57, 87, 201, 201, 201, 201, 201, 19, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 19, 19, 19, 19, 19, 57, 57, 201, 19, 19, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 491 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: REAL300025478267 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 104, 50, 50, 50, 50, 36, 31, 36, 11, 1, 1, 1, 1, 1, 1, 1, 50, 111, 201, 201, 201, 201, 201, 201, 111, 111, 111, 104, 104, 50, 50, 50, 50, 50, 31, 31, 1, 50, 50, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 738 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478267 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478267 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478267/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478267 Building REAL300025478268 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478268' /scratch/stefan/7787258/working/building/REAL300025478268 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478268 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478268/0 /scratch/stefan/7787258/working/building/REAL300025478268 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/131 `/scratch/stefan/7787258/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCCO1) `REAL300025478268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478268 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 62, 62, 62, 62, 62, 1, 15, 29, 29, 44, 44, 44, 44, 44, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 9, 9, 62, 1, 1, 44, 44, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478268 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 33, 44, 44, 44, 44, 52, 52, 98, 120, 201, 201, 201, 201, 201, 44, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 33, 33, 44, 44, 44, 44, 44, 98, 98, 201, 44, 44, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 589 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478268 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 121, 62, 62, 62, 62, 51, 41, 51, 13, 1, 1, 1, 1, 1, 1, 1, 62, 144, 181, 181, 201, 201, 201, 201, 201, 144, 144, 144, 121, 121, 62, 62, 62, 62, 62, 41, 41, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478268 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478268 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478268/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478268 Building REAL300025478269 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478269' /scratch/stefan/7787258/working/building/REAL300025478269 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478269 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478269/0 /scratch/stefan/7787258/working/building/REAL300025478269 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/132 `/scratch/stefan/7787258/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCS1) `REAL300025478269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478269 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 6, 6, 13, 20, 62, 62, 62, 62, 62, 1, 13, 28, 28, 43, 43, 43, 43, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 62, 1, 1, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478269 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 16, 30, 43, 43, 43, 43, 65, 65, 108, 125, 201, 201, 201, 201, 201, 43, 1, 9, 1, 1, 1, 1, 1, 16, 16, 16, 30, 30, 43, 43, 43, 43, 43, 108, 108, 201, 43, 43, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478269 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 124, 62, 62, 62, 62, 50, 41, 50, 13, 1, 1, 1, 1, 1, 1, 1, 62, 145, 164, 164, 201, 201, 201, 201, 145, 145, 145, 124, 124, 62, 62, 62, 62, 62, 41, 41, 1, 62, 62, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478269 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478269 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478269/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478269 Building REAL300025478270 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478270' /scratch/stefan/7787258/working/building/REAL300025478270 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478270 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478270/0 /scratch/stefan/7787258/working/building/REAL300025478270 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/133 `/scratch/stefan/7787258/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478270 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 14, 21, 21, 21, 21, 37, 37, 72, 106, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 21, 21, 21, 21, 21, 72, 72, 201, 21, 21, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 46, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 495 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: REAL300025478270 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 194, 198, 162, 194, 84, 84, 84, 84, 54, 43, 54, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 194, 194, 194, 162, 162, 84, 84, 84, 84, 84, 43, 43, 1, 84, 84, 201, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 779 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: REAL300025478270 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 15, 12, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 84, 84, 84, 84, 84, 1, 21, 21, 21, 21, 21, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 15, 15, 84, 1, 1, 21, 21] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46]) total number of confs: 214 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478270 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478270 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478270/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478270 Building REAL300025478271 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478271' /scratch/stefan/7787258/working/building/REAL300025478271 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478271 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478271/0 /scratch/stefan/7787258/working/building/REAL300025478271 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/134 `/scratch/stefan/7787258/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(=O)NC1CC1) `REAL300025478271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478271 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 72, 72, 72, 72, 72, 1, 8, 11, 11, 17, 17, 17, 37, 37, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 7, 7, 72, 1, 1, 17, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478271 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 12, 24, 34, 37, 37, 37, 37, 50, 50, 79, 117, 201, 201, 201, 201, 201, 37, 6, 14, 6, 6, 1, 1, 1, 1, 26, 26, 26, 34, 34, 37, 37, 37, 37, 37, 79, 79, 201, 37, 37, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478271 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 128, 72, 72, 72, 72, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 72, 168, 179, 179, 188, 188, 188, 201, 201, 168, 168, 168, 128, 128, 72, 72, 72, 72, 72, 30, 30, 1, 72, 72, 188, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478271 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478271 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478271/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478271 Building REAL300025478272 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478272' /scratch/stefan/7787258/working/building/REAL300025478272 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478272 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478272/0 /scratch/stefan/7787258/working/building/REAL300025478272 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/135 `/scratch/stefan/7787258/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478272 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 8, 8, 8, 8, 20, 20, 38, 61, 187, 187, 187, 187, 187, 8, 1, 9, 9, 9, 9, 9, 1, 2, 2, 2, 4, 4, 8, 8, 8, 8, 8, 38, 38, 187, 8, 8, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 49, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478272 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 187, 187, 187, 187, 187, 187, 171, 187, 87, 87, 87, 87, 57, 40, 57, 13, 1, 1, 1, 1, 1, 1, 1, 87, 187, 201, 201, 201, 201, 201, 187, 187, 187, 187, 171, 171, 87, 87, 87, 87, 87, 40, 40, 1, 87, 87, 187, 187] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 814 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478272 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 87, 87, 87, 87, 87, 1, 8, 24, 24, 24, 24, 24, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 14, 14, 87, 1, 1, 8, 8] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478272 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478272 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478272/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478272 Building REAL300025478273 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478273' /scratch/stefan/7787258/working/building/REAL300025478273 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478273 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478273/0 /scratch/stefan/7787258/working/building/REAL300025478273 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/136 `/scratch/stefan/7787258/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSC1) `REAL300025478273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478273 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 69, 69, 69, 69, 69, 1, 13, 24, 24, 33, 33, 33, 33, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 69, 1, 1, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 231 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: REAL300025478273 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 26, 33, 33, 33, 33, 44, 44, 89, 116, 201, 201, 201, 201, 201, 33, 1, 6, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 33, 33, 33, 33, 33, 89, 89, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 555 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: REAL300025478273 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 131, 69, 69, 69, 69, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 69, 147, 188, 188, 201, 201, 201, 201, 147, 147, 147, 131, 131, 69, 69, 69, 69, 69, 39, 39, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478273 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478273 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478273/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478273 Building REAL300025478274 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478274' /scratch/stefan/7787258/working/building/REAL300025478274 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478274 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478274/0 /scratch/stefan/7787258/working/building/REAL300025478274 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/137 `/scratch/stefan/7787258/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCO1) `REAL300025478274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478274 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 6, 6, 14, 22, 70, 70, 70, 70, 70, 1, 12, 21, 21, 22, 22, 22, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 14, 14, 70, 1, 1, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478274 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 5, 7, 15, 22, 22, 22, 22, 39, 39, 72, 106, 201, 201, 201, 201, 201, 22, 1, 5, 1, 1, 1, 1, 7, 7, 7, 15, 15, 22, 22, 22, 22, 22, 72, 72, 201, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478274 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 139, 70, 70, 70, 70, 49, 41, 49, 13, 1, 1, 1, 1, 1, 1, 1, 70, 170, 199, 199, 201, 201, 201, 170, 170, 170, 139, 139, 70, 70, 70, 70, 70, 41, 41, 1, 70, 70, 201, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478274 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478274 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478274/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478274 Building REAL300025478275 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478275' /scratch/stefan/7787258/working/building/REAL300025478275 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478275 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478275/0 /scratch/stefan/7787258/working/building/REAL300025478275 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/138 `/scratch/stefan/7787258/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCN=[N+]=[N-]) `REAL300025478275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478275 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 43, 43, 43, 43, 43, 1, 10, 15, 15, 15, 15, 37, 37, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 6, 6, 43, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478275 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 8, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 106, 43, 43, 43, 43, 26, 22, 26, 10, 1, 1, 1, 1, 1, 1, 1, 43, 132, 164, 164, 164, 164, 201, 201, 132, 132, 132, 106, 106, 43, 43, 43, 43, 43, 22, 22, 1, 43, 43, 164, 164, 164, 164] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478275 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478275 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478275/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478275 Building REAL300025478276 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478276' /scratch/stefan/7787258/working/building/REAL300025478276 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478276 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478276/0 /scratch/stefan/7787258/working/building/REAL300025478276 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/139 `/scratch/stefan/7787258/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478276 none C#CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 30, 25, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 51, 51, 51, 51, 51, 1, 41, 41, 41, 25, 25, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 51, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478276 none C#CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 190, 187, 111, 111, 111, 98, 111, 51, 51, 51, 51, 37, 34, 37, 13, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 187, 187, 111, 111, 111, 98, 98, 51, 51, 51, 51, 51, 34, 34, 1, 51, 51] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 898 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478276 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478276 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478276/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478276 Building REAL300025478277 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478277' /scratch/stefan/7787258/working/building/REAL300025478277 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478277 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478277/0 /scratch/stefan/7787258/working/building/REAL300025478277 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/140 `/scratch/stefan/7787258/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CO1) `REAL300025478277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478277 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 49, 49, 49, 49, 49, 1, 13, 23, 23, 34, 41, 41, 41, 41, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 49, 1, 1, 34, 34, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 231 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: REAL300025478277 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 19, 31, 41, 41, 41, 41, 58, 58, 100, 129, 201, 201, 201, 201, 201, 41, 3, 12, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 31, 41, 41, 41, 41, 41, 100, 100, 201, 41, 41, 3, 3, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 597 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: REAL300025478277 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 106, 49, 49, 49, 49, 39, 34, 39, 12, 1, 1, 1, 1, 1, 1, 1, 49, 127, 158, 158, 172, 201, 201, 201, 201, 127, 127, 127, 106, 106, 49, 49, 49, 49, 49, 34, 34, 1, 49, 49, 172, 172, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 729 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478277 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478277 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478277/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478277 Building REAL300025478278 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478278' /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478278 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478278/0 /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/141 `/scratch/stefan/7787258/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478278 none CN(CCO)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 27, 38, 47, 51, 13, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 4, 4, 11, 19, 74, 74, 74, 74, 74, 1, 38, 38, 38, 47, 47, 51, 51, 153, 27, 27, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 74, 1, 1] 603 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 494 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: REAL300025478278 none CN(CCO)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 198, 201, 201, 201, 165, 165, 165, 143, 165, 74, 74, 74, 74, 58, 44, 58, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 201, 603, 198, 198, 165, 165, 165, 143, 143, 74, 74, 74, 74, 74, 44, 44, 1, 74, 74] 603 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 1421 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478278/1 /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/142 `/scratch/stefan/7787258/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@H+](C)CCO) `REAL300025478278.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478278 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@H+](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 7, 7, 7, 7, 7, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 4, 4, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 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: REAL300025478278 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@H+](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24] 24 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 36 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478278/2 /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/143 `/scratch/stefan/7787258/working/3D/143' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@@H+](C)CCO) `REAL300025478278.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478278/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478278 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@@H+](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 7, 7, 7, 7, 7, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 4, 4, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21] 21 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478278 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[N@@H+](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21] 21 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 29 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478278 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478278 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478278/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478278/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478278/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478278 Building REAL300025478279 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478279' /scratch/stefan/7787258/working/building/REAL300025478279 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478279 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478279/0 /scratch/stefan/7787258/working/building/REAL300025478279 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/144 `/scratch/stefan/7787258/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCS1) `REAL300025478279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478279 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 81, 81, 81, 81, 81, 1, 11, 20, 20, 32, 32, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 15, 81, 1, 1, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 248 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: REAL300025478279 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 27, 32, 32, 32, 32, 47, 47, 91, 120, 201, 201, 201, 201, 201, 32, 1, 6, 1, 1, 1, 1, 1, 15, 15, 15, 27, 27, 32, 32, 32, 32, 32, 91, 91, 201, 32, 32, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 568 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: REAL300025478279 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 152, 81, 81, 81, 81, 57, 47, 57, 13, 1, 1, 1, 1, 1, 1, 1, 81, 170, 192, 192, 201, 201, 201, 201, 170, 170, 170, 152, 152, 81, 81, 81, 81, 81, 47, 47, 1, 81, 81, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478279 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478279 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478279/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478279 Building REAL300025478280 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478280' /scratch/stefan/7787258/working/building/REAL300025478280 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478280 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478280/0 /scratch/stefan/7787258/working/building/REAL300025478280 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/145 `/scratch/stefan/7787258/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)O) `REAL300025478280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478280 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 48, 48, 48, 48, 48, 1, 10, 19, 19, 23, 23, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 7, 7, 48, 1, 1, 23, 23, 23, 23, 23, 23, 69] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 232 number of broken/clashed sets: 455 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478280 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [129, 91, 48, 48, 48, 48, 30, 27, 30, 11, 1, 1, 1, 1, 1, 1, 1, 48, 129, 172, 172, 201, 201, 201, 129, 129, 129, 91, 91, 48, 48, 48, 48, 48, 27, 27, 1, 48, 48, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1402 number of broken/clashed sets: 455 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478280 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478280 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478280/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478280 Building REAL300025478281 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478281' /scratch/stefan/7787258/working/building/REAL300025478281 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478281 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478281/0 /scratch/stefan/7787258/working/building/REAL300025478281 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/146 `/scratch/stefan/7787258/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=CC=N1) `REAL300025478281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478281 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 60, 60, 60, 60, 60, 1, 13, 25, 25, 41, 46, 46, 46, 46, 46, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 60, 1, 1, 41, 41, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 282 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478281 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 21, 36, 46, 46, 46, 46, 54, 54, 97, 120, 201, 201, 201, 201, 201, 46, 5, 13, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 36, 36, 46, 46, 46, 46, 46, 97, 97, 201, 46, 46, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478281 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 109, 60, 60, 60, 60, 46, 36, 46, 12, 1, 1, 1, 1, 1, 1, 1, 60, 142, 184, 184, 194, 201, 201, 201, 201, 201, 142, 142, 142, 109, 109, 60, 60, 60, 60, 60, 36, 36, 1, 60, 60, 194, 194, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 762 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478281 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478281 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478281/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478281 Building REAL300025478282 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478282' /scratch/stefan/7787258/working/building/REAL300025478282 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478282 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478282/0 /scratch/stefan/7787258/working/building/REAL300025478282 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/147 `/scratch/stefan/7787258/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CN=C1F) `REAL300025478282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478282 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 13, 19, 61, 61, 61, 61, 61, 1, 14, 29, 29, 40, 40, 40, 40, 40, 40, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 61, 1, 1, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478282 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 29, 40, 40, 40, 40, 59, 59, 103, 125, 201, 201, 201, 201, 201, 40, 1, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 29, 29, 40, 40, 40, 40, 40, 103, 103, 201, 40, 40, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478282 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 127, 61, 61, 61, 61, 49, 39, 49, 13, 1, 1, 1, 1, 1, 1, 1, 61, 142, 178, 178, 201, 201, 201, 201, 201, 201, 142, 142, 142, 127, 127, 61, 61, 61, 61, 61, 39, 39, 1, 61, 61, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478282 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478282 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478282/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478282 Building REAL300025478283 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478283' /scratch/stefan/7787258/working/building/REAL300025478283 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478283 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478283/0 /scratch/stefan/7787258/working/building/REAL300025478283 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/148 `/scratch/stefan/7787258/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478283 none CC1=CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 9, 9, 22, 32, 32, 32, 32, 46, 46, 83, 117, 201, 201, 201, 201, 201, 32, 2, 2, 2, 1, 1, 9, 9, 9, 22, 22, 32, 32, 32, 32, 32, 83, 83, 201, 32, 32] 201 rigid atoms, others: [0, 1, 2, 3, 4, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478283 none CC1=CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 135, 137, 118, 135, 57, 57, 57, 57, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 135, 135, 135, 118, 118, 57, 57, 57, 57, 57, 36, 36, 1, 57, 57] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 780 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478283 none CC1=CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 15, 12, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 13, 21, 57, 57, 57, 57, 57, 1, 32, 32, 32, 32, 32, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 57, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478283 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478283 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478283/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478283 Building REAL300025478284 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478284' /scratch/stefan/7787258/working/building/REAL300025478284 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478284 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478284/0 /scratch/stefan/7787258/working/building/REAL300025478284 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/149 `/scratch/stefan/7787258/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478284 none CN(C)C(=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 14, 26, 10, 14, 5, 10, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 64, 64, 64, 64, 64, 1, 26, 26, 26, 26, 26, 26, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 8, 8, 64, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478284 none CN(C)C(=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 201, 163, 173, 135, 163, 64, 64, 64, 64, 51, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 163, 163, 163, 135, 135, 64, 64, 64, 64, 64, 30, 30, 1, 64, 64] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478284 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478284 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478284/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478284 Building REAL300025478285 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478285' /scratch/stefan/7787258/working/building/REAL300025478285 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478285 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478285/0 /scratch/stefan/7787258/working/building/REAL300025478285 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/150 `/scratch/stefan/7787258/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478285 none CSC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 38, 13, 13, 13, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 73, 73, 73, 73, 73, 1, 48, 48, 48, 38, 38, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 73, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 242 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: REAL300025478285 none CSC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 161, 161, 161, 138, 161, 73, 73, 73, 73, 56, 41, 56, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 161, 161, 161, 138, 138, 73, 73, 73, 73, 73, 41, 41, 1, 73, 73] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 762 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478285 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478285 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478285/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478285 Building REAL300025478286 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478286' /scratch/stefan/7787258/working/building/REAL300025478286 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478286 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478286/0 /scratch/stefan/7787258/working/building/REAL300025478286 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/151 `/scratch/stefan/7787258/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=CC1=O) `REAL300025478286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478286 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 13, 36, 36, 36, 36, 36, 1, 13, 19, 19, 25, 25, 25, 25, 25, 25, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 36, 1, 1, 25, 25, 25, 25] 89 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478286 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 18, 25, 25, 25, 25, 31, 31, 50, 59, 89, 89, 89, 89, 89, 25, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 18, 18, 25, 25, 25, 25, 25, 50, 50, 89, 25, 25, 1, 1, 1, 1] 89 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 272 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478286 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [75, 65, 36, 36, 36, 36, 32, 29, 32, 13, 1, 1, 1, 1, 1, 1, 1, 36, 75, 81, 81, 89, 89, 89, 89, 89, 89, 75, 75, 75, 65, 65, 36, 36, 36, 36, 36, 29, 29, 1, 36, 36, 89, 89, 89, 89] 89 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478286 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478286 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478286/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478286 Building REAL300025478287 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478287' /scratch/stefan/7787258/working/building/REAL300025478287 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478287 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478287/0 /scratch/stefan/7787258/working/building/REAL300025478287 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/152 `/scratch/stefan/7787258/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CS1) `REAL300025478287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478287 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 9, 9, 20, 36, 36, 36, 36, 52, 52, 90, 119, 201, 201, 201, 201, 201, 36, 1, 1, 2, 2, 2, 1, 9, 9, 9, 20, 20, 36, 36, 36, 36, 36, 90, 90, 201, 36, 36, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478287 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 172, 179, 143, 172, 73, 73, 73, 73, 54, 42, 54, 12, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 172, 172, 172, 143, 143, 73, 73, 73, 73, 73, 42, 42, 1, 73, 73, 201, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 776 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478287 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 21, 14, 21, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 73, 73, 73, 73, 73, 1, 36, 36, 36, 36, 36, 36, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 73, 1, 1, 36, 36] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478287 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478287 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478287/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478287 Building REAL300025478288 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478288' /scratch/stefan/7787258/working/building/REAL300025478288 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478288 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478288/0 /scratch/stefan/7787258/working/building/REAL300025478288 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/153 `/scratch/stefan/7787258/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478288 none CCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 13, 21, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 71, 71, 71, 71, 71, 1, 23, 23, 23, 23, 23, 21, 21, 21, 63, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 71, 1, 1] 603 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478288 none CCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 154, 201, 121, 154, 71, 71, 71, 71, 49, 42, 49, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 603, 154, 154, 154, 121, 121, 71, 71, 71, 71, 71, 42, 42, 1, 71, 71] 603 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1378 number of broken/clashed sets: 203 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478288 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478288 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478288/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478288 Building REAL300025478289 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478289' /scratch/stefan/7787258/working/building/REAL300025478289 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478289 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478289/0 /scratch/stefan/7787258/working/building/REAL300025478289 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/154 `/scratch/stefan/7787258/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478289 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 18, 18, 18, 18, 30, 30, 45, 65, 131, 131, 131, 131, 131, 18, 1, 7, 7, 7, 7, 7, 4, 4, 4, 12, 12, 18, 18, 18, 18, 18, 45, 45, 131, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478289 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 131, 131, 131, 123, 123, 123, 114, 123, 59, 59, 59, 59, 42, 33, 42, 12, 1, 1, 1, 1, 1, 1, 1, 59, 131, 201, 201, 201, 201, 201, 123, 123, 123, 114, 114, 59, 59, 59, 59, 59, 33, 33, 1, 59, 59] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 909 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478289 none CCC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 18, 18, 18, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 59, 59, 59, 59, 59, 1, 18, 33, 33, 33, 33, 33, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 11, 11, 59, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478289 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478289 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478289/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478289 Building REAL300025478290 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478290' /scratch/stefan/7787258/working/building/REAL300025478290 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478290 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478290/0 /scratch/stefan/7787258/working/building/REAL300025478290 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/155 `/scratch/stefan/7787258/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C[NH+](C)C) `REAL300025478290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478290 none CC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 18, 18, 18, 18, 18, 1, 6, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 6, 6, 18, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 18 rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 43, 48, 40, 22, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478290 none CC(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 18, 12, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478290 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478290 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478290/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478290 Building REAL300025478291 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478291' /scratch/stefan/7787258/working/building/REAL300025478291 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478291 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478291/0 /scratch/stefan/7787258/working/building/REAL300025478291 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/156 `/scratch/stefan/7787258/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1) `REAL300025478291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478291 none CC1=NN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 52, 64, 64, 64, 64, 88, 88, 120, 144, 201, 201, 201, 201, 201, 64, 1, 1, 2, 2, 2, 9, 9, 28, 28, 28, 52, 52, 64, 64, 64, 64, 64, 120, 120, 201, 64, 64] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478291 none CC1=NN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 81, 81, 81, 78, 81, 44, 44, 44, 44, 38, 34, 38, 13, 1, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 138, 138, 81, 81, 81, 78, 78, 44, 44, 44, 44, 44, 34, 34, 1, 44, 44] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 689 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478291 none CC1=NN(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 26, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 5, 5, 11, 15, 44, 44, 44, 44, 44, 1, 64, 64, 64, 64, 64, 26, 26, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 11, 11, 44, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478291 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478291 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478291/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478291 Building REAL300025478292 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478292' /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478292 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478292/0 /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/157 `/scratch/stefan/7787258/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478292 none CC[N@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 7, 12, 12, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 7, 8, 18, 18, 18, 18, 18, 1, 15, 15, 15, 15, 15, 12, 12, 12, 7, 7, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 7, 7, 18, 1, 1] 28 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 107 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478292 none CC[N@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 26, 28, 28, 23, 23, 23, 21, 23, 18, 18, 18, 18, 18, 16, 18, 12, 1, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 28, 28, 28, 28, 28, 26, 26, 23, 23, 23, 21, 21, 18, 18, 18, 18, 18, 16, 16, 1, 18, 18] 28 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 98 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478292/1 /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/158 `/scratch/stefan/7787258/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478292.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478292 none CC[N@@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 8, 11, 11, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 12, 12, 12, 12, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 6, 6, 12, 1, 1] 18 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 74 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478292 none CC[N@@H+](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 15, 15, 15, 13, 15, 12, 12, 12, 12, 12, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 15, 13, 13, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 18 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 55 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478292/2 /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/159 `/scratch/stefan/7787258/working/3D/159' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478292.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478292 none CCN(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 39, 30, 39, 18, 15, 18, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 64, 64, 64, 64, 64, 1, 40, 40, 40, 40, 40, 39, 39, 39, 30, 30, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 12, 12, 64, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478292 none CCN(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 154, 146, 154, 128, 146, 64, 64, 64, 64, 44, 36, 44, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 146, 146, 128, 128, 64, 64, 64, 64, 64, 36, 36, 1, 64, 64] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478292 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478292 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478292/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478292/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478292/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478292 Building REAL300025478293 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478293' /scratch/stefan/7787258/working/building/REAL300025478293 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478293 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478293/0 /scratch/stefan/7787258/working/building/REAL300025478293 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/160 `/scratch/stefan/7787258/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)F) `REAL300025478293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478293 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 34, 34, 34, 34, 34, 1, 12, 19, 19, 19, 19, 33, 33, 33, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 34, 1, 1, 19, 19, 19, 19, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478293 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 34, 34, 34, 34, 23, 21, 23, 11, 1, 1, 1, 1, 1, 1, 1, 34, 113, 144, 144, 144, 144, 201, 201, 201, 113, 113, 113, 88, 88, 34, 34, 34, 34, 34, 21, 21, 1, 34, 34, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478293 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478293 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478293/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478293 Building REAL300025478294 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478294' /scratch/stefan/7787258/working/building/REAL300025478294 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478294 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478294/0 /scratch/stefan/7787258/working/building/REAL300025478294 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/161 `/scratch/stefan/7787258/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025478294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478294 none CC[C@H](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 36, 30, 36, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 58, 58, 58, 58, 58, 1, 36, 39, 40, 39, 39, 39, 39, 39, 30, 30, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1, 40, 39, 40, 40, 40, 40, 40] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 301 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478294 none CC[C@H](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 194, 199, 110, 110, 110, 103, 110, 58, 58, 58, 58, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 58, 199, 200, 201, 201, 201, 201, 201, 201, 194, 194, 110, 110, 110, 103, 103, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58, 201, 200, 201, 201, 201, 201, 201] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 845 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478294 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478294 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478294/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478294 Building REAL300025478295 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478295' /scratch/stefan/7787258/working/building/REAL300025478295 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478295 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478295/0 /scratch/stefan/7787258/working/building/REAL300025478295 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/162 `/scratch/stefan/7787258/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478295 none CCC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 51, 51, 51, 51, 51, 1, 43, 43, 43, 43, 43, 22, 22, 22, 22, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 12, 51, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 278 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: REAL300025478295 none CCC=CC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 127, 127, 127, 127, 87, 87, 87, 85, 87, 51, 51, 51, 51, 44, 34, 44, 13, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 127, 127, 127, 127, 87, 87, 87, 85, 85, 51, 51, 51, 51, 51, 34, 34, 1, 51, 51] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 928 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478295 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478295 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478295/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478295 Building REAL300025478296 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478296' /scratch/stefan/7787258/working/building/REAL300025478296 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478296 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478296/0 /scratch/stefan/7787258/working/building/REAL300025478296 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/163 `/scratch/stefan/7787258/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(=CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478296 none CC1CCC(=CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 26, 42, 42, 42, 42, 52, 52, 92, 112, 201, 201, 201, 201, 201, 42, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 42, 42, 42, 42, 42, 92, 92, 201, 42, 42, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 51, 34, 35, 52, 26, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 571 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: REAL300025478296 none CC1CCC(=CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 140, 135, 140, 118, 135, 60, 60, 60, 60, 50, 37, 50, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 118, 118, 60, 60, 60, 60, 60, 37, 37, 1, 60, 60, 201, 201] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 782 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: REAL300025478296 none CC1CCC(=CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 15, 12, 15, 6, 12, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 60, 60, 60, 60, 60, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 9, 9, 60, 1, 1, 42, 42] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52]) total number of confs: 228 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478296 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478296 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478296/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478296 Building REAL300025478297 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478297' /scratch/stefan/7787258/working/building/REAL300025478297 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478297 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478297/0 /scratch/stefan/7787258/working/building/REAL300025478297 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/164 `/scratch/stefan/7787258/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N[N-]1) `REAL300025478297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478297 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 3, 3, 11, 18, 64, 64, 64, 64, 64, 1, 17, 36, 36, 41, 41, 41, 41, 41, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 64, 1, 1, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478297 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 28, 41, 41, 41, 41, 48, 48, 89, 116, 201, 201, 201, 201, 201, 41, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 28, 41, 41, 41, 41, 41, 89, 89, 201, 41, 41, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 572 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478297 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 64, 64, 64, 64, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 64, 150, 194, 194, 201, 201, 201, 201, 201, 150, 150, 150, 122, 122, 64, 64, 64, 64, 64, 36, 36, 1, 64, 64, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478297 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478297 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478297/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478297 Building REAL300025478298 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478298' /scratch/stefan/7787258/working/building/REAL300025478298 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478298 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478298/0 /scratch/stefan/7787258/working/building/REAL300025478298 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/165 `/scratch/stefan/7787258/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1) `REAL300025478298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478298 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 14, 14, 29, 45, 45, 45, 45, 52, 52, 92, 114, 201, 201, 201, 201, 201, 45, 1, 1, 2, 2, 2, 1, 14, 14, 14, 29, 29, 45, 45, 45, 45, 45, 92, 92, 201, 45, 45, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478298 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 139, 152, 123, 139, 58, 58, 58, 58, 49, 38, 49, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 139, 139, 139, 123, 123, 58, 58, 58, 58, 58, 38, 38, 1, 58, 58, 201, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 706 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: REAL300025478298 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 18, 11, 18, 6, 11, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 58, 58, 58, 58, 58, 1, 45, 45, 45, 45, 45, 45, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 9, 9, 58, 1, 1, 45, 45] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46]) total number of confs: 195 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478298 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478298 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478298/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478298 Building REAL300025478299 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478299' /scratch/stefan/7787258/working/building/REAL300025478299 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478299 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478299/0 /scratch/stefan/7787258/working/building/REAL300025478299 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/166 `/scratch/stefan/7787258/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478299 none COCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 26, 20, 20, 20, 20, 13, 20, 5, 13, 1, 1, 1, 1, 1, 1, 4, 4, 12, 18, 62, 62, 62, 62, 62, 1, 33, 33, 33, 26, 26, 20, 20, 20, 60, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 62, 1, 1] 603 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 283 number of broken/clashed sets: 202 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478299 none COCC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 165, 165, 165, 165, 152, 165, 132, 152, 62, 62, 62, 62, 43, 34, 43, 12, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 165, 165, 165, 495, 152, 152, 152, 132, 132, 62, 62, 62, 62, 62, 34, 34, 1, 62, 62] 603 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 1342 number of broken/clashed sets: 202 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478299 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478299 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478299/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478299 Building REAL300025478300 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478300' /scratch/stefan/7787258/working/building/REAL300025478300 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478300 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478300/0 /scratch/stefan/7787258/working/building/REAL300025478300 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/167 `/scratch/stefan/7787258/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478300 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 5, 5, 13, 23, 23, 23, 23, 40, 40, 73, 110, 201, 201, 201, 201, 201, 23, 1, 1, 1, 2, 2, 2, 5, 5, 5, 13, 13, 23, 23, 23, 23, 23, 73, 73, 201, 23, 23, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 518 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478300 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 120, 120, 108, 120, 56, 56, 56, 56, 41, 36, 41, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 120, 120, 120, 108, 108, 56, 56, 56, 56, 56, 36, 36, 1, 56, 56, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 624 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: REAL300025478300 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 7, 13, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 56, 56, 56, 56, 56, 1, 23, 23, 23, 23, 23, 23, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 14, 14, 56, 1, 1, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478300 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478300 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478300/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478300 Building REAL300025478301 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478301' /scratch/stefan/7787258/working/building/REAL300025478301 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478301 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478301/0 /scratch/stefan/7787258/working/building/REAL300025478301 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/168 `/scratch/stefan/7787258/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478301 none C=C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 12, 12, 28, 46, 46, 46, 46, 65, 65, 108, 140, 201, 201, 201, 201, 201, 46, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 28, 46, 46, 46, 46, 46, 108, 108, 201, 46, 46, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 24, 25, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478301 none C=C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 164, 170, 149, 164, 79, 79, 79, 79, 59, 44, 59, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 164, 164, 164, 149, 149, 79, 79, 79, 79, 79, 44, 44, 1, 79, 79, 201, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 777 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478301 none C=C1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 20, 14, 20, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 23, 79, 79, 79, 79, 79, 1, 46, 46, 46, 46, 46, 46, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 79, 1, 1, 46, 46] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 43, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478301 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478301 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478301/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478301 Building REAL300025478302 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478302' /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478302 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478302/0 /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/169 `/scratch/stefan/7787258/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478302 none CC[N@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 5, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 3, 3, 5, 1, 1, 4, 4, 4, 4, 4] 5 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CC[N@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1] 5 rigid atoms, others: [2, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 21 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CC[N@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478302/1 /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/170 `/scratch/stefan/7787258/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478302.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478302 none CC[N@@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 6, 6, 6, 6, 6, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 5, 5, 6, 1, 1, 5, 5, 5, 5, 5] 6 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CC[N@@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 1, 3, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1] 6 rigid atoms, others: [2, 50, 51, 52, 53, 54, 25, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 32 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: REAL300025478302 none CC[N@@H+](CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 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, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 12 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478302/2 /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/171 `/scratch/stefan/7787258/working/3D/171' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478302.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478302/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CCN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 23, 13, 12, 13, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 81, 81, 81, 81, 81, 1, 25, 31, 31, 25, 25, 25, 25, 25, 23, 23, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 15, 15, 81, 1, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52, 53]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CCN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 6, 9, 9, 10, 10, 20, 31, 31, 31, 31, 45, 45, 75, 111, 201, 201, 201, 201, 201, 31, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 20, 20, 31, 31, 31, 31, 31, 75, 75, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 49, 50, 51, 52, 53, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 526 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478302 none CCN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 195, 193, 195, 167, 193, 81, 81, 81, 81, 53, 42, 53, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 167, 167, 81, 81, 81, 81, 81, 42, 42, 1, 81, 81, 201, 201, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478302 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478302 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478302/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478302/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478302/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478302 Building REAL300025478303 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478303' /scratch/stefan/7787258/working/building/REAL300025478303 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478303 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478303/0 /scratch/stefan/7787258/working/building/REAL300025478303 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/172 `/scratch/stefan/7787258/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CC1) `REAL300025478303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478303 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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: [18, 7, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 62, 62, 62, 62, 62, 1, 18, 27, 27, 29, 29, 29, 31, 31, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 11, 11, 62, 1, 1, 29, 29, 29, 87, 31, 31, 31, 31, 31] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 299 number of broken/clashed sets: 366 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478303 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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, 5, 9, 19, 31, 31, 31, 31, 40, 40, 75, 108, 201, 201, 201, 201, 201, 31, 4, 5, 1, 4, 4, 1, 1, 1, 9, 9, 9, 19, 19, 31, 31, 31, 31, 31, 75, 75, 201, 31, 31, 4, 4, 4, 12, 1, 1, 1, 1, 1] 603 rigid atoms, others: [45, 46, 47, 48, 49, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 544 number of broken/clashed sets: 366 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478303 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 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: [164, 126, 62, 62, 62, 62, 45, 38, 45, 13, 1, 1, 1, 1, 1, 1, 1, 62, 164, 200, 200, 200, 200, 200, 201, 201, 164, 164, 164, 126, 126, 62, 62, 62, 62, 62, 38, 38, 1, 62, 62, 200, 200, 200, 600, 201, 201, 201, 201, 201] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1371 number of broken/clashed sets: 366 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478303 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478303 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478303/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478303 Building REAL300025478304 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478304' /scratch/stefan/7787258/working/building/REAL300025478304 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478304 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478304/0 /scratch/stefan/7787258/working/building/REAL300025478304 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/173 `/scratch/stefan/7787258/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478304 none CC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 21, 33, 33, 33, 33, 48, 48, 88, 117, 201, 201, 201, 201, 201, 33, 1, 2, 2, 2, 1, 11, 11, 11, 21, 21, 33, 33, 33, 33, 33, 88, 88, 201, 33, 33] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478304 none CC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 190, 199, 170, 190, 80, 80, 80, 80, 52, 40, 52, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 190, 190, 190, 170, 170, 80, 80, 80, 80, 80, 40, 40, 1, 80, 80] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 768 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478304 none CC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 22, 15, 22, 7, 15, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 80, 80, 80, 80, 80, 1, 33, 33, 33, 33, 33, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 16, 16, 80, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478304 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478304 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478304/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478304 Building REAL300025478305 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478305' /scratch/stefan/7787258/working/building/REAL300025478305 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478305 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478305/0 /scratch/stefan/7787258/working/building/REAL300025478305 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/174 `/scratch/stefan/7787258/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NNC=C1Cl) `REAL300025478305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478305 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NNC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 21, 21, 21, 21, 21, 1, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 5, 5, 21, 1, 1, 9, 9] 34 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478305 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NNC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 7, 9, 9, 9, 9, 9, 9, 17, 22, 34, 34, 34, 34, 34, 9, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 9, 9, 9, 9, 9, 17, 17, 34, 9, 9, 1, 1] 34 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478305 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NNC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 21, 21, 21, 21, 21, 20, 21, 10, 1, 1, 1, 1, 1, 1, 1, 21, 27, 27, 27, 34, 34, 34, 34, 34, 27, 27, 27, 26, 26, 21, 21, 21, 21, 21, 20, 20, 1, 21, 21, 34, 34] 34 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478305 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478305 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478305/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478305 Building REAL300025478306 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478306' /scratch/stefan/7787258/working/building/REAL300025478306 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478306 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478306/0 /scratch/stefan/7787258/working/building/REAL300025478306 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/175 `/scratch/stefan/7787258/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CS1) `REAL300025478306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478306 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 16, 26, 26, 26, 26, 39, 39, 75, 106, 201, 201, 201, 201, 201, 26, 1, 1, 1, 2, 2, 2, 7, 7, 7, 16, 16, 26, 26, 26, 26, 26, 75, 75, 201, 26, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478306 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 160, 162, 128, 160, 53, 53, 53, 53, 40, 33, 40, 13, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 160, 160, 160, 128, 128, 53, 53, 53, 53, 53, 33, 33, 1, 53, 53, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 691 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478306 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 16, 12, 16, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 53, 53, 53, 53, 53, 1, 26, 26, 26, 26, 26, 26, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 12, 12, 53, 1, 1, 26] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478306 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478306 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478306/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478306 Building REAL300025478307 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478307' /scratch/stefan/7787258/working/building/REAL300025478307 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478307 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478307/0 /scratch/stefan/7787258/working/building/REAL300025478307 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/176 `/scratch/stefan/7787258/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC1F) `REAL300025478307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478307 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 71, 71, 71, 71, 71, 1, 16, 29, 29, 41, 41, 41, 41, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 13, 13, 71, 1, 1, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 258 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: REAL300025478307 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 29, 41, 41, 41, 41, 61, 61, 100, 128, 201, 201, 201, 201, 201, 41, 1, 6, 1, 1, 1, 1, 1, 13, 13, 13, 29, 29, 41, 41, 41, 41, 41, 100, 100, 201, 41, 41, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 578 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: REAL300025478307 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 138, 71, 71, 71, 71, 49, 40, 49, 13, 1, 1, 1, 1, 1, 1, 1, 71, 169, 191, 191, 201, 201, 201, 201, 169, 169, 169, 138, 138, 71, 71, 71, 71, 71, 40, 40, 1, 71, 71, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 753 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478307 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478307 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478307/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478307 Building REAL300025478308 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478308' /scratch/stefan/7787258/working/building/REAL300025478308 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478308 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478308/0 /scratch/stefan/7787258/working/building/REAL300025478308 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/177 `/scratch/stefan/7787258/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478308 none CC[NH+](CC)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 25, 35, 35, 40, 22, 14, 12, 14, 6, 12, 1, 1, 1, 1, 1, 1, 2, 2, 10, 16, 71, 71, 71, 71, 71, 1, 38, 38, 38, 38, 38, 40, 40, 40, 40, 40, 25, 25, 22, 22, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 10, 10, 71, 1, 1] 201 rigid atoms, others: [16, 17, 47, 12, 13, 14, 15, 48, 49, 50, 51, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 52, 53, 54]) total number of confs: 321 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478308 none CC[NH+](CC)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 192, 144, 126, 144, 108, 126, 71, 71, 71, 71, 61, 34, 61, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 126, 126, 126, 108, 108, 71, 71, 71, 71, 71, 34, 34, 1, 71, 71] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 844 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478308 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478308 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478308/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478308 Building REAL300025478309 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478309' /scratch/stefan/7787258/working/building/REAL300025478309 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478309 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478309/0 /scratch/stefan/7787258/working/building/REAL300025478309 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/178 `/scratch/stefan/7787258/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=N1) `REAL300025478309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 63, 63, 63, 63, 63, 1, 15, 32, 32, 37, 37, 37, 37, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 12, 12, 63, 1, 1, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 27, 37, 37, 37, 37, 49, 49, 82, 112, 201, 201, 201, 201, 201, 37, 1, 7, 1, 1, 1, 1, 1, 16, 16, 16, 27, 27, 37, 37, 37, 37, 37, 82, 82, 201, 37, 37, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 129, 63, 63, 63, 63, 49, 41, 49, 13, 1, 1, 1, 1, 1, 1, 1, 63, 175, 198, 198, 201, 201, 201, 201, 175, 175, 175, 129, 129, 63, 63, 63, 63, 63, 41, 41, 1, 63, 63, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478309 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478309/1 /scratch/stefan/7787258/working/building/REAL300025478309 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/179 `/scratch/stefan/7787258/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CN1) `REAL300025478309.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 12, 33, 33, 33, 33, 33, 1, 11, 21, 21, 25, 25, 25, 25, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 10, 10, 33, 1, 1, 25, 25, 25] 52 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 141 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: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 16, 22, 25, 25, 25, 25, 31, 31, 38, 43, 52, 52, 52, 52, 52, 25, 1, 10, 1, 1, 1, 1, 1, 16, 16, 16, 22, 22, 25, 25, 25, 25, 25, 38, 38, 52, 25, 25, 1, 1, 1] 52 rigid atoms, others: [40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478309 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 47, 33, 33, 33, 33, 32, 31, 32, 13, 1, 1, 1, 1, 1, 1, 1, 33, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 47, 47, 33, 33, 33, 33, 33, 31, 31, 1, 33, 33, 52, 52, 52] 52 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478309 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478309 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478309/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478309/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478309 Building REAL300025478310 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478310' /scratch/stefan/7787258/working/building/REAL300025478310 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478310 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478310/0 /scratch/stefan/7787258/working/building/REAL300025478310 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/180 `/scratch/stefan/7787258/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478310 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 21, 33, 33, 33, 33, 49, 49, 91, 121, 201, 201, 201, 201, 201, 33, 1, 2, 2, 2, 13, 13, 13, 21, 21, 33, 33, 33, 33, 33, 91, 91, 201, 33, 33] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478310 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 190, 182, 190, 161, 182, 80, 80, 80, 80, 54, 41, 54, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 182, 182, 182, 161, 161, 80, 80, 80, 80, 80, 41, 41, 1, 80, 80] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 733 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478310 none CC1=NOC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 19, 14, 19, 7, 14, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 80, 80, 80, 80, 80, 1, 33, 33, 33, 33, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 14, 14, 80, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478310 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478310 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478310/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478310 Building REAL300025478311 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478311' /scratch/stefan/7787258/working/building/REAL300025478311 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478311 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478311/0 /scratch/stefan/7787258/working/building/REAL300025478311 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/181 `/scratch/stefan/7787258/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CC2C1) `REAL300025478311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478311 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 13, 22, 67, 67, 67, 67, 67, 1, 13, 25, 25, 33, 33, 33, 33, 33, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 67, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 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: REAL300025478311 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 24, 33, 33, 33, 33, 40, 40, 85, 113, 201, 201, 201, 201, 201, 33, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 24, 24, 33, 33, 33, 33, 33, 85, 85, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 533 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: REAL300025478311 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 134, 67, 67, 67, 67, 49, 40, 49, 13, 1, 1, 1, 1, 1, 1, 1, 67, 156, 193, 193, 201, 201, 201, 201, 201, 156, 156, 156, 134, 134, 67, 67, 67, 67, 67, 40, 40, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 784 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478311 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478311 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478311/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478311 Building REAL300025478312 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478312' /scratch/stefan/7787258/working/building/REAL300025478312 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478312 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478312/0 /scratch/stefan/7787258/working/building/REAL300025478312 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/182 `/scratch/stefan/7787258/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CN=C1) `REAL300025478312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478312 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 14, 19, 51, 51, 51, 51, 51, 1, 14, 29, 29, 39, 39, 39, 39, 39, 39, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 51, 1, 1, 39, 39, 39, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 244 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: REAL300025478312 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 11, 14, 28, 37, 37, 37, 37, 62, 62, 107, 133, 201, 201, 201, 201, 201, 37, 4, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 28, 37, 37, 37, 37, 37, 107, 107, 201, 37, 37, 4, 4, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 589 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: REAL300025478312 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 51, 51, 51, 51, 42, 34, 42, 13, 1, 1, 1, 1, 1, 1, 1, 51, 142, 190, 190, 201, 201, 201, 201, 201, 201, 142, 142, 142, 111, 111, 51, 51, 51, 51, 51, 34, 34, 1, 51, 51, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 774 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478312 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478312 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478312/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478312 Building REAL300025478313 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478313' /scratch/stefan/7787258/working/building/REAL300025478313 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478313 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478313/0 /scratch/stefan/7787258/working/building/REAL300025478313 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/183 `/scratch/stefan/7787258/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478313 none CC1=NSC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 15, 15, 31, 45, 45, 45, 45, 66, 66, 110, 136, 201, 201, 201, 201, 201, 45, 1, 2, 2, 2, 15, 15, 15, 31, 31, 45, 45, 45, 45, 45, 110, 110, 201, 45, 45, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478313 none CC1=NSC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 173, 160, 173, 135, 160, 71, 71, 71, 71, 57, 43, 57, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 160, 160, 160, 135, 135, 71, 71, 71, 71, 71, 43, 43, 1, 71, 71, 201] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 734 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478313 none CC1=NSC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 21, 13, 21, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 71, 71, 71, 71, 71, 1, 45, 45, 45, 45, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 71, 1, 1, 45] 201 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478313 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478313 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478313/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478313 Building REAL300025478314 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478314' /scratch/stefan/7787258/working/building/REAL300025478314 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478314 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478314/0 /scratch/stefan/7787258/working/building/REAL300025478314 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/184 `/scratch/stefan/7787258/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCSC1) `REAL300025478314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478314 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 14, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 67, 67, 67, 67, 67, 1, 13, 30, 30, 40, 40, 40, 40, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 67, 1, 1, 40, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478314 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 14, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 29, 40, 40, 40, 40, 59, 59, 102, 126, 201, 201, 201, 201, 201, 40, 1, 8, 1, 1, 1, 1, 1, 14, 14, 14, 29, 29, 40, 40, 40, 40, 40, 102, 102, 201, 40, 40, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 575 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: REAL300025478314 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 14, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 128, 67, 67, 67, 67, 55, 42, 55, 13, 1, 1, 1, 1, 1, 1, 1, 67, 155, 186, 186, 201, 201, 201, 201, 155, 155, 155, 128, 128, 67, 67, 67, 67, 67, 42, 42, 1, 67, 67, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 729 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478314 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478314 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478314/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478314 Building REAL300025478315 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478315' /scratch/stefan/7787258/working/building/REAL300025478315 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478315 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478315/0 /scratch/stefan/7787258/working/building/REAL300025478315 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/185 `/scratch/stefan/7787258/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCC(F)F) `REAL300025478315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478315 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 54, 54, 54, 54, 54, 1, 11, 19, 19, 20, 22, 24, 45, 45, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1, 20, 20, 22, 22, 24, 24, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478315 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 119, 54, 54, 54, 54, 36, 28, 36, 13, 1, 1, 1, 1, 1, 1, 1, 54, 165, 196, 196, 198, 200, 201, 201, 201, 165, 165, 165, 119, 119, 54, 54, 54, 54, 54, 28, 28, 1, 54, 54, 198, 198, 200, 200, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478315 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478315 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478315/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478315 Building REAL300025478316 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478316' /scratch/stefan/7787258/working/building/REAL300025478316 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478316 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478316/0 /scratch/stefan/7787258/working/building/REAL300025478316 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/186 `/scratch/stefan/7787258/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC(C)(C)C1) `REAL300025478316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 69, 69, 69, 69, 69, 1, 11, 21, 21, 29, 33, 33, 33, 33, 33, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 69, 1, 1, 29, 29, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 240 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: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 19, 29, 33, 33, 33, 33, 43, 43, 86, 111, 201, 201, 201, 201, 201, 33, 5, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 29, 29, 33, 33, 33, 33, 33, 86, 86, 201, 33, 33, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [44, 45, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 563 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: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 137, 69, 69, 69, 69, 49, 39, 49, 13, 1, 1, 1, 1, 1, 1, 1, 69, 159, 187, 187, 199, 201, 201, 201, 201, 201, 159, 159, 159, 137, 137, 69, 69, 69, 69, 69, 39, 39, 1, 69, 69, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 787 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478316 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478316/1 /scratch/stefan/7787258/working/building/REAL300025478316 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/187 `/scratch/stefan/7787258/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC(C)(C)C1) `REAL300025478316.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 13, 13, 13, 13, 13, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 13, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 8, 11, 11, 11, 11, 13, 13, 17, 17, 18, 18, 18, 18, 18, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 11, 11, 11, 11, 11, 17, 17, 18, 11, 11, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 18 rigid atoms, others: [54, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478316 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 13, 13, 13, 13, 13, 12, 13, 11, 1, 1, 1, 1, 1, 1, 1, 13, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 16, 15, 15, 13, 13, 13, 13, 13, 12, 12, 1, 13, 13, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478316 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478316 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478316/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478316/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478316 Building REAL300025478317 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478317' /scratch/stefan/7787258/working/building/REAL300025478317 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478317 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478317/0 /scratch/stefan/7787258/working/building/REAL300025478317 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/188 `/scratch/stefan/7787258/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478317 none CCCC(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 34, 21, 34, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 81, 81, 81, 81, 81, 1, 39, 39, 39, 39, 39, 39, 39, 34, 102, 21, 21, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 16, 16, 81, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478317 none CCCC(O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 200, 177, 200, 162, 162, 162, 147, 162, 81, 81, 81, 81, 58, 44, 58, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 200, 600, 177, 177, 162, 162, 162, 147, 147, 81, 81, 81, 81, 81, 44, 44, 1, 81, 81] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478317 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478317 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478317/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478317 Building REAL300025478318 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478318' /scratch/stefan/7787258/working/building/REAL300025478318 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478318 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478318/0 /scratch/stefan/7787258/working/building/REAL300025478318 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/189 `/scratch/stefan/7787258/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(Cl)CC1) `REAL300025478318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478318 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 42, 42, 42, 42, 42, 1, 10, 21, 21, 35, 35, 35, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478318 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 24, 35, 35, 35, 35, 45, 45, 67, 94, 201, 201, 201, 201, 201, 35, 1, 5, 1, 1, 1, 1, 11, 11, 11, 24, 24, 35, 35, 35, 35, 35, 67, 67, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478318 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 16, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 82, 42, 42, 42, 42, 29, 25, 29, 12, 1, 1, 1, 1, 1, 1, 1, 42, 122, 169, 169, 201, 201, 201, 122, 122, 122, 82, 82, 42, 42, 42, 42, 42, 25, 25, 1, 42, 42, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478318 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478318 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478318/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478318 Building REAL300025478319 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478319' /scratch/stefan/7787258/working/building/REAL300025478319 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478319 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478319/0 /scratch/stefan/7787258/working/building/REAL300025478319 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/190 `/scratch/stefan/7787258/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCO1) `REAL300025478319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478319 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 63, 63, 63, 63, 63, 1, 16, 29, 29, 35, 35, 35, 35, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 10, 10, 63, 1, 1, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478319 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 26, 35, 35, 35, 35, 44, 44, 80, 108, 201, 201, 201, 201, 201, 35, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 35, 35, 35, 35, 35, 80, 80, 201, 35, 35, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 537 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478319 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 129, 63, 63, 63, 63, 49, 40, 49, 12, 1, 1, 1, 1, 1, 1, 1, 63, 159, 189, 189, 201, 201, 201, 201, 159, 159, 159, 129, 129, 63, 63, 63, 63, 63, 40, 40, 1, 63, 63, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478319 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478319 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478319/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478319 Building REAL300025478320 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478320' /scratch/stefan/7787258/working/building/REAL300025478320 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478320 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478320/0 /scratch/stefan/7787258/working/building/REAL300025478320 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/191 `/scratch/stefan/7787258/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(CO)O1) `REAL300025478320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478320 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 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: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 23, 81, 81, 81, 81, 81, 1, 15, 21, 21, 23, 23, 23, 23, 43, 23, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 13, 13, 81, 1, 1, 23, 23, 43, 43, 129] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 433 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: REAL300025478320 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 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, 5, 9, 16, 23, 23, 23, 23, 34, 34, 64, 96, 201, 201, 201, 201, 201, 23, 1, 5, 1, 1, 1, 1, 1, 8, 1, 9, 9, 9, 16, 16, 23, 23, 23, 23, 23, 64, 64, 201, 23, 23, 1, 1, 8, 8, 24] 603 rigid atoms, others: [42, 43, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 520 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: REAL300025478320 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(CO)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 5, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 3, 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: [190, 154, 81, 81, 81, 81, 59, 40, 59, 13, 1, 1, 1, 1, 1, 1, 1, 81, 190, 200, 200, 201, 201, 201, 201, 201, 201, 190, 190, 190, 154, 154, 81, 81, 81, 81, 81, 40, 40, 1, 81, 81, 201, 201, 201, 201, 603] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1374 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478320 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478320 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478320/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478320 Building REAL300025478321 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478321' /scratch/stefan/7787258/working/building/REAL300025478321 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478321 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478321/0 /scratch/stefan/7787258/working/building/REAL300025478321 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/192 `/scratch/stefan/7787258/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)F) `REAL300025478321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478321 none CC(=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 11, 13, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 67, 67, 67, 67, 67, 1, 28, 47, 47, 28, 28, 28, 28, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 67, 1, 1, 47] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45]) total number of confs: 288 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: REAL300025478321 none CC(=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 137, 134, 137, 118, 134, 67, 67, 67, 67, 55, 44, 55, 13, 1, 1, 1, 1, 1, 1, 1, 67, 198, 201, 201, 198, 198, 198, 198, 134, 134, 134, 118, 118, 67, 67, 67, 67, 67, 44, 44, 1, 67, 67, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478321 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478321 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478321/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478321 Building REAL300025478322 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478322' /scratch/stefan/7787258/working/building/REAL300025478322 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478322 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478322/0 /scratch/stefan/7787258/working/building/REAL300025478322 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/193 `/scratch/stefan/7787258/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC2(CC2)C1) `REAL300025478322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478322 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 46, 46, 46, 46, 46, 1, 16, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 7, 7, 46, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 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: REAL300025478322 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 16, 31, 31, 31, 31, 39, 39, 68, 105, 201, 201, 201, 201, 201, 31, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 31, 31, 31, 31, 31, 68, 68, 201, 31, 31, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478322 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 110, 46, 46, 46, 46, 34, 27, 34, 12, 1, 1, 1, 1, 1, 1, 1, 46, 134, 201, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 110, 110, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 750 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478322 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478322 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478322/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478322 Building REAL300025478323 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478323' /scratch/stefan/7787258/working/building/REAL300025478323 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478323 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478323/0 /scratch/stefan/7787258/working/building/REAL300025478323 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/194 `/scratch/stefan/7787258/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC[NH+](C)C) `REAL300025478323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478323 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 5, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 27 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: REAL300025478323 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 6 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478323 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478323 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478323/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478323 Building REAL300025478324 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478324' /scratch/stefan/7787258/working/building/REAL300025478324 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478324 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478324/0 /scratch/stefan/7787258/working/building/REAL300025478324 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/195 `/scratch/stefan/7787258/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478324 none CCC[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 45, 22, 10, 22, 22, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 15, 21, 58, 58, 58, 58, 58, 1, 46, 46, 46, 46, 46, 45, 45, 66, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 15, 15, 58, 1, 1] 603 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478324 none CCC[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 169, 120, 169, 169, 120, 120, 102, 120, 58, 58, 58, 58, 50, 39, 50, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 507, 120, 120, 120, 102, 102, 58, 58, 58, 58, 58, 39, 39, 1, 58, 58] 603 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478324 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478324 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478324/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478324 Building REAL300025478325 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478325' /scratch/stefan/7787258/working/building/REAL300025478325 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478325 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478325/0 /scratch/stefan/7787258/working/building/REAL300025478325 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/196 `/scratch/stefan/7787258/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1) `REAL300025478325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478325 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 6, 6, 19, 32, 32, 32, 32, 41, 41, 68, 105, 201, 201, 201, 201, 201, 32, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 32, 32, 32, 32, 32, 68, 68, 201, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 525 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: REAL300025478325 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 134, 178, 120, 134, 54, 54, 54, 54, 36, 25, 36, 12, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 134, 134, 134, 120, 120, 54, 54, 54, 54, 54, 25, 25, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) 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: REAL300025478325 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 23, 13, 23, 6, 13, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 54, 54, 54, 54, 54, 1, 32, 32, 32, 32, 32, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478325 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478325 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478325/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478325 Building REAL300025478326 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478326' /scratch/stefan/7787258/working/building/REAL300025478326 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478326 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478326/0 /scratch/stefan/7787258/working/building/REAL300025478326 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/197 `/scratch/stefan/7787258/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1COCCO1) `REAL300025478326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478326 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 57, 57, 57, 57, 57, 1, 14, 25, 25, 28, 36, 36, 36, 36, 36, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 57, 1, 1, 28, 28, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478326 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 26, 36, 36, 36, 36, 52, 52, 93, 117, 201, 201, 201, 201, 201, 36, 5, 9, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 36, 36, 36, 36, 36, 93, 93, 201, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478326 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1COCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 124, 57, 57, 57, 57, 38, 32, 38, 11, 1, 1, 1, 1, 1, 1, 1, 57, 150, 187, 187, 192, 201, 201, 201, 201, 201, 150, 150, 150, 124, 124, 57, 57, 57, 57, 57, 32, 32, 1, 57, 57, 192, 192, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478326 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478326 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478326/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478326 Building REAL300025478327 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478327' /scratch/stefan/7787258/working/building/REAL300025478327 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478327 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478327/0 /scratch/stefan/7787258/working/building/REAL300025478327 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/198 `/scratch/stefan/7787258/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1) `REAL300025478327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478327 none CC(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 3, 3, 3, 3, 10, 18, 18, 18, 18, 27, 27, 51, 93, 201, 201, 201, 201, 201, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 10, 10, 18, 18, 18, 18, 18, 51, 51, 201, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 49, 50, 51, 52, 24, 25, 26] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 495 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478327 none CC(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 158, 201, 117, 158, 64, 64, 64, 64, 46, 26, 46, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 117, 117, 64, 64, 64, 64, 64, 26, 26, 1, 64, 64, 201, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 773 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478327 none CC(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 11, 18, 6, 11, 1, 1, 1, 1, 1, 1, 2, 2, 9, 18, 64, 64, 64, 64, 64, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 9, 9, 64, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478327 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478327 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478327/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478327 Building REAL300025478328 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478328' /scratch/stefan/7787258/working/building/REAL300025478328 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478328 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478328/0 /scratch/stefan/7787258/working/building/REAL300025478328 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/199 `/scratch/stefan/7787258/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478328 none CNC(=O)N[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 26, 26, 26, 19, 12, 19, 19, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 56, 56, 56, 56, 56, 1, 35, 35, 35, 35, 26, 19, 19, 19, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 56, 1, 1] 201 rigid atoms, others: [45, 49, 41, 42, 43, 12, 13, 14, 15, 16, 17, 50, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 237 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: REAL300025478328 none CNC(=O)N[C@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 164, 188, 188, 164, 164, 128, 164, 56, 56, 56, 56, 37, 31, 37, 12, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 188, 188, 188, 164, 164, 164, 128, 128, 56, 56, 56, 56, 56, 31, 31, 1, 56, 56] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 819 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478328 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478328 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478328/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478328 Building REAL300025478329 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478329' /scratch/stefan/7787258/working/building/REAL300025478329 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478329 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478329/0 /scratch/stefan/7787258/working/building/REAL300025478329 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/200 `/scratch/stefan/7787258/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(C)CCCO1) `REAL300025478329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478329 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 51, 51, 51, 51, 51, 1, 11, 22, 22, 31, 32, 32, 32, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 51, 1, 1, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 220 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: REAL300025478329 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 18, 28, 32, 32, 32, 32, 43, 43, 87, 112, 201, 201, 201, 201, 201, 32, 6, 10, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 28, 28, 32, 32, 32, 32, 32, 87, 87, 201, 32, 32, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 582 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: REAL300025478329 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(C)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 111, 51, 51, 51, 51, 35, 32, 35, 12, 1, 1, 1, 1, 1, 1, 1, 51, 124, 167, 167, 201, 201, 201, 201, 201, 201, 124, 124, 124, 111, 111, 51, 51, 51, 51, 51, 32, 32, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 822 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478329 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478329 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478329/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478329 Building REAL300025478330 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478330' /scratch/stefan/7787258/working/building/REAL300025478330 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478330 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478330/0 /scratch/stefan/7787258/working/building/REAL300025478330 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/201 `/scratch/stefan/7787258/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1) `REAL300025478330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478330 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 5, 13, 25, 25, 25, 25, 43, 43, 84, 117, 201, 201, 201, 201, 201, 25, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 13, 13, 25, 25, 25, 25, 25, 84, 84, 201, 25, 25, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478330 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 171, 179, 146, 171, 73, 73, 73, 73, 54, 45, 54, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 146, 146, 73, 73, 73, 73, 73, 45, 45, 1, 73, 73, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 730 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478330 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 19, 14, 19, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 73, 73, 73, 73, 73, 1, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 15, 15, 73, 1, 1, 25, 25, 25, 25] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478330 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478330 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478330/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478330 Building REAL300025478331 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478331' /scratch/stefan/7787258/working/building/REAL300025478331 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478331 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478331/0 /scratch/stefan/7787258/working/building/REAL300025478331 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/202 `/scratch/stefan/7787258/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CS1) `REAL300025478331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478331 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 58, 58, 58, 58, 58, 1, 12, 21, 21, 31, 35, 35, 35, 35, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 58, 1, 1, 31, 31, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 230 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: REAL300025478331 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 16, 26, 35, 35, 35, 35, 52, 52, 98, 123, 201, 201, 201, 201, 201, 35, 2, 10, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 26, 35, 35, 35, 35, 35, 98, 98, 201, 35, 35, 2, 2, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 588 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: REAL300025478331 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 118, 58, 58, 58, 58, 46, 36, 46, 13, 1, 1, 1, 1, 1, 1, 1, 58, 138, 169, 169, 175, 201, 201, 201, 201, 138, 138, 138, 118, 118, 58, 58, 58, 58, 58, 36, 36, 1, 58, 58, 175, 175, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 738 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478331 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478331 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478331/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478331 Building REAL300025478332 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478332' /scratch/stefan/7787258/working/building/REAL300025478332 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478332 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478332/0 /scratch/stefan/7787258/working/building/REAL300025478332 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/203 `/scratch/stefan/7787258/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12) `REAL300025478332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478332 none CO[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 12, 22, 22, 22, 22, 33, 33, 54, 88, 201, 201, 201, 201, 201, 22, 1, 1, 1, 5, 5, 5, 1, 1, 6, 6, 6, 12, 12, 22, 22, 22, 22, 22, 54, 54, 201, 22, 22, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 50, 26, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478332 none CO[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 200, 180, 200, 146, 180, 63, 63, 63, 63, 42, 31, 42, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 146, 146, 63, 63, 63, 63, 63, 31, 31, 1, 63, 63, 201, 201] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 773 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478332 none CO[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 22, 22, 22, 21, 15, 21, 6, 15, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 63, 63, 63, 63, 63, 1, 22, 22, 22, 39, 39, 39, 22, 22, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 8, 8, 63, 1, 1, 22, 22] 201 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478332 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478332 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478332/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478332 Building REAL300025478333 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478333' /scratch/stefan/7787258/working/building/REAL300025478333 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478333 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478333/0 /scratch/stefan/7787258/working/building/REAL300025478333 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/204 `/scratch/stefan/7787258/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CN1C) `REAL300025478333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478333 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 79, 79, 79, 79, 79, 1, 13, 25, 25, 38, 40, 40, 40, 40, 40, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 79, 1, 1, 38, 38, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 286 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478333 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 19, 32, 40, 40, 40, 40, 54, 54, 91, 120, 201, 201, 201, 201, 201, 40, 3, 12, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 32, 32, 40, 40, 40, 40, 40, 91, 91, 201, 40, 40, 3, 3, 1, 2, 2, 2] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 576 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478333 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 1, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 133, 79, 79, 79, 79, 55, 42, 55, 13, 1, 1, 1, 1, 1, 1, 1, 79, 162, 194, 194, 201, 201, 201, 201, 201, 201, 162, 162, 162, 133, 133, 79, 79, 79, 79, 79, 42, 42, 1, 79, 79, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 782 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478333 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478333 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478333/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478333 Building REAL300025478334 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478334' /scratch/stefan/7787258/working/building/REAL300025478334 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478334 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478334/0 /scratch/stefan/7787258/working/building/REAL300025478334 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/205 `/scratch/stefan/7787258/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NON=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478334 none CCC1=NON=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 24, 24, 24, 24, 34, 34, 59, 69, 120, 120, 120, 120, 120, 24, 5, 5, 5, 4, 4, 5, 5, 5, 11, 11, 24, 24, 24, 24, 24, 59, 59, 120, 24, 24] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478334 none CCC1=NON=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 120, 120, 120, 120, 120, 106, 106, 106, 89, 106, 46, 46, 46, 46, 37, 33, 37, 12, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 106, 106, 106, 89, 89, 46, 46, 46, 46, 46, 33, 33, 1, 46, 46] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 921 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478334 none CCC1=NON=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 24, 24, 24, 24, 24, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 4, 4, 10, 15, 46, 46, 46, 46, 46, 1, 45, 45, 45, 45, 45, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 46, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478334 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478334 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478334/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478334 Building REAL300025478335 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478335' /scratch/stefan/7787258/working/building/REAL300025478335 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478335 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478335/0 /scratch/stefan/7787258/working/building/REAL300025478335 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/206 `/scratch/stefan/7787258/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NSN=C1) `REAL300025478335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478335 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 54, 54, 54, 54, 54, 1, 14, 24, 24, 36, 40, 40, 40, 40, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 54, 1, 1, 36, 36, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 247 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: REAL300025478335 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 30, 40, 40, 40, 40, 58, 58, 104, 128, 201, 201, 201, 201, 201, 40, 3, 10, 1, 1, 1, 1, 1, 1, 20, 20, 20, 30, 30, 40, 40, 40, 40, 40, 104, 104, 201, 40, 40, 3, 3, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 586 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: REAL300025478335 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 112, 54, 54, 54, 54, 42, 35, 42, 13, 1, 1, 1, 1, 1, 1, 1, 54, 138, 171, 171, 185, 201, 201, 201, 201, 138, 138, 138, 112, 112, 54, 54, 54, 54, 54, 35, 35, 1, 54, 54, 185, 185, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 774 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478335 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478335 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478335/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478335 Building REAL300025478336 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478336' /scratch/stefan/7787258/working/building/REAL300025478336 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478336 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478336/0 /scratch/stefan/7787258/working/building/REAL300025478336 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/207 `/scratch/stefan/7787258/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478336 none C=CCC(C)(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 33, 12, 33, 33, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 40, 40, 40, 40, 40, 1, 57, 57, 57, 44, 44, 33, 33, 33, 33, 33, 33, 12, 12, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 9, 9, 40, 1, 1] 201 rigid atoms, others: [16, 15, 11, 12, 13, 14, 45, 48, 49, 46, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478336 none C=CCC(C)(C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 91, 176, 176, 62, 62, 62, 60, 62, 40, 40, 40, 40, 33, 29, 33, 13, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 176, 176, 176, 176, 176, 176, 91, 91, 62, 62, 62, 60, 60, 40, 40, 40, 40, 40, 29, 29, 1, 40, 40] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478336 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478336 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478336/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478336 Building REAL300025478337 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478337' /scratch/stefan/7787258/working/building/REAL300025478337 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478337 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478337/0 /scratch/stefan/7787258/working/building/REAL300025478337 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/208 `/scratch/stefan/7787258/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478337 none CCC(C)(OC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 21, 22, 22, 22, 13, 21, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 62, 62, 62, 62, 62, 1, 25, 25, 25, 25, 25, 22, 22, 22, 22, 22, 22, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 12, 12, 62, 1, 1] 201 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478337 none CCC(C)(OC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 201, 201, 201, 147, 199, 126, 147, 62, 62, 62, 62, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 126, 126, 62, 62, 62, 62, 62, 35, 35, 1, 62, 62] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478337 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478337 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478337/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478337 Building REAL300025478338 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478338' /scratch/stefan/7787258/working/building/REAL300025478338 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478338 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478338/0 /scratch/stefan/7787258/working/building/REAL300025478338 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/209 `/scratch/stefan/7787258/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478338 none CC(C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 31, 41, 17, 31, 31, 14, 17, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 61, 61, 61, 61, 61, 1, 41, 41, 41, 41, 41, 41, 41, 93, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 61, 1, 1] 603 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478338 none CC(C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 184, 201, 129, 184, 184, 127, 129, 114, 127, 61, 61, 61, 61, 50, 40, 50, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 201, 552, 127, 127, 127, 114, 114, 61, 61, 61, 61, 61, 40, 40, 1, 61, 61] 603 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478338 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478338 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478338/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478338 Building REAL300025478339 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478339' /scratch/stefan/7787258/working/building/REAL300025478339 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478339 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478339/0 /scratch/stefan/7787258/working/building/REAL300025478339 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/210 `/scratch/stefan/7787258/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478339 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 5, 5, 7, 7, 16, 27, 27, 27, 27, 42, 42, 76, 105, 201, 201, 201, 201, 201, 27, 1, 1, 1, 5, 5, 5, 7, 7, 7, 16, 16, 27, 27, 27, 27, 27, 76, 76, 201, 27, 27, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478339 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 128, 157, 115, 128, 55, 55, 55, 55, 43, 34, 43, 11, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 201, 128, 128, 128, 115, 115, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 790 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478339 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 27, 19, 10, 19, 5, 10, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 55, 55, 55, 55, 55, 1, 27, 27, 27, 36, 36, 36, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 55, 1, 1, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478339 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478339 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478339/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478339 Building REAL300025478340 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478340' /scratch/stefan/7787258/working/building/REAL300025478340 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478340 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478340/0 /scratch/stefan/7787258/working/building/REAL300025478340 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/211 `/scratch/stefan/7787258/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478340 none CC(CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 5, 5, 5, 5, 5, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 5, 1, 1, 3, 3, 3, 3, 3, 3] 6 rigid atoms, others: [43, 8, 9, 10, 11, 12, 45, 44, 50, 49, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 28 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478340 none CC(CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [48, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 17 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478340 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478340 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478340/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478340 Building REAL300025478341 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478341' /scratch/stefan/7787258/working/building/REAL300025478341 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478341 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478341/0 /scratch/stefan/7787258/working/building/REAL300025478341 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/212 `/scratch/stefan/7787258/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CC(F)=N1) `REAL300025478341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478341 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 66, 66, 66, 66, 66, 1, 16, 33, 33, 38, 38, 38, 38, 38, 38, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 10, 10, 66, 1, 1, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478341 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 26, 38, 38, 38, 38, 49, 49, 81, 106, 201, 201, 201, 201, 201, 38, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 38, 38, 38, 38, 38, 81, 81, 201, 38, 38, 1, 1] 201 rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 538 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478341 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 124, 66, 66, 66, 66, 47, 39, 47, 12, 1, 1, 1, 1, 1, 1, 1, 66, 153, 199, 199, 201, 201, 201, 201, 201, 201, 153, 153, 153, 124, 124, 66, 66, 66, 66, 66, 39, 39, 1, 66, 66, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478341 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478341 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478341/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478341 Building REAL300025478342 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478342' /scratch/stefan/7787258/working/building/REAL300025478342 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478342 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478342/0 /scratch/stefan/7787258/working/building/REAL300025478342 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/213 `/scratch/stefan/7787258/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478342 none CC(C)C(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 25, 30, 12, 25, 44, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 22, 73, 73, 73, 73, 73, 1, 30, 30, 30, 30, 30, 30, 30, 25, 44, 44, 132, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 73, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 475 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478342 none CC(C)C(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 197, 201, 167, 197, 201, 167, 167, 136, 167, 73, 73, 73, 73, 54, 41, 54, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 197, 201, 201, 603, 167, 167, 167, 136, 136, 73, 73, 73, 73, 73, 41, 41, 1, 73, 73] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1456 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478342 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478342 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478342/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478342 Building REAL300025478343 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478343' /scratch/stefan/7787258/working/building/REAL300025478343 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478343 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478343/0 /scratch/stefan/7787258/working/building/REAL300025478343 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/214 `/scratch/stefan/7787258/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478343 none CCOC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 71, 71, 71, 71, 71, 1, 49, 49, 49, 49, 49, 37, 37, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 71, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 241 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: REAL300025478343 none CCOC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 156, 156, 135, 156, 71, 71, 71, 71, 55, 43, 55, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 135, 135, 71, 71, 71, 71, 71, 43, 43, 1, 71, 71] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 779 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478343 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478343 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478343/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478343 Building REAL300025478344 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478344' /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478344 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478344/0 /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/215 `/scratch/stefan/7787258/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478344 none CCN1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 24, 43, 43, 43, 43, 61, 61, 100, 124, 201, 201, 201, 201, 201, 43, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 24, 24, 43, 43, 43, 43, 43, 100, 100, 201, 43, 43] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 586 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: REAL300025478344 none CCN1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 171, 159, 171, 139, 159, 72, 72, 72, 72, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 139, 139, 72, 72, 72, 72, 72, 42, 42, 1, 72, 72] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 778 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: REAL300025478344 none CCN1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 43, 43, 43, 43, 23, 16, 23, 6, 16, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 72, 72, 72, 72, 72, 1, 46, 46, 46, 46, 46, 43, 43, 43, 43, 43, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 15, 15, 72, 1, 1] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 284 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478344/1 /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/216 `/scratch/stefan/7787258/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478344.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478344 none CC[N@@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 10, 12, 12, 12, 12, 14, 14, 22, 22, 30, 30, 30, 30, 30, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 12, 12, 12, 12, 12, 22, 22, 30, 12, 12] 30 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478344 none CC[N@@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 29, 29, 29, 25, 29, 22, 22, 22, 22, 21, 20, 21, 12, 1, 1, 1, 1, 1, 1, 1, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 29, 25, 25, 22, 22, 22, 22, 22, 20, 20, 1, 22, 22] 30 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478344 none CC[N@@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 12, 12, 12, 12, 12, 7, 6, 7, 3, 6, 1, 1, 1, 1, 1, 1, 5, 5, 8, 9, 22, 22, 22, 22, 22, 1, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 8, 8, 22, 1, 1] 30 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478344/2 /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/217 `/scratch/stefan/7787258/working/3D/217' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478344.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478344/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478344 none CC[N@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 10, 10, 10, 10, 12, 12, 15, 15, 16, 16, 16, 16, 16, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 10, 10, 10, 15, 15, 16, 10, 10] 16 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 72 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: REAL300025478344 none CC[N@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 16, 12, 12, 12, 12, 12, 11, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 12, 12, 12, 12, 12, 11, 11, 1, 12, 12] 16 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 39 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: REAL300025478344 none CC[N@H+]1CCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 12, 12, 12, 12, 12, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 6, 6, 12, 1, 1] 16 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478344 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478344 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478344/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478344/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478344/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478344 Building REAL300025478345 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478345' /scratch/stefan/7787258/working/building/REAL300025478345 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478345 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478345/0 /scratch/stefan/7787258/working/building/REAL300025478345 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/218 `/scratch/stefan/7787258/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCCC1) `REAL300025478345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478345 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 66, 66, 66, 66, 66, 1, 14, 23, 23, 25, 25, 25, 25, 25, 25, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 66, 1, 1, 25, 25, 75, 25, 25, 25, 25, 25, 25, 25, 25] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 279 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: REAL300025478345 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [8, 3, 8, 16, 25, 25, 25, 25, 45, 45, 86, 113, 201, 201, 201, 201, 201, 25, 2, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 25, 25, 25, 25, 25, 86, 86, 201, 25, 25, 2, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 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: REAL300025478345 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [157, 138, 66, 66, 66, 66, 46, 38, 46, 13, 1, 1, 1, 1, 1, 1, 1, 66, 157, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 138, 138, 66, 66, 66, 66, 66, 38, 38, 1, 66, 66, 201, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1354 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478345 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478345 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478345/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478345 Building REAL300025478346 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478346' /scratch/stefan/7787258/working/building/REAL300025478346 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478346 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478346/0 /scratch/stefan/7787258/working/building/REAL300025478346 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/219 `/scratch/stefan/7787258/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC1O) `REAL300025478346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478346 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 6, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 99, 99, 99, 99, 99, 1, 15, 22, 22, 26, 26, 26, 26, 26, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 16, 16, 99, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 78] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 330 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: REAL300025478346 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 9, 15, 26, 26, 26, 26, 37, 37, 77, 108, 201, 201, 201, 201, 201, 26, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 26, 26, 26, 26, 26, 77, 77, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 3] 603 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49]) total number of confs: 534 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: REAL300025478346 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [190, 174, 99, 99, 99, 99, 69, 50, 69, 13, 1, 1, 1, 1, 1, 1, 1, 99, 190, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 174, 174, 99, 99, 99, 99, 99, 50, 50, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1363 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478346 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478346 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478346/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478346 Building REAL300025478347 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478347' /scratch/stefan/7787258/working/building/REAL300025478347 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478347 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478347/0 /scratch/stefan/7787258/working/building/REAL300025478347 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/220 `/scratch/stefan/7787258/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478347 none C[C@@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 22, 34, 34, 14, 22, 6, 14, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 63, 63, 63, 63, 63, 1, 34, 34, 34, 102, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 5, 5, 63, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 328 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478347 none C[C@@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 189, 201, 201, 152, 189, 108, 152, 63, 63, 63, 63, 42, 32, 42, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 603, 152, 152, 152, 108, 108, 63, 63, 63, 63, 63, 32, 32, 1, 63, 63] 603 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 1389 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478347 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478347 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478347/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478347 Building REAL300025478348 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478348' /scratch/stefan/7787258/working/building/REAL300025478348 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478348 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478348/0 /scratch/stefan/7787258/working/building/REAL300025478348 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/221 `/scratch/stefan/7787258/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478348 none CSSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 36, 21, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 58, 58, 58, 58, 58, 1, 46, 46, 46, 21, 21, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478348 none CSSCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 157, 118, 118, 118, 104, 118, 58, 58, 58, 58, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 157, 157, 118, 118, 118, 104, 104, 58, 58, 58, 58, 58, 35, 35, 1, 58, 58] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478348 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478348 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478348/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478348 Building REAL300025478349 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478349' /scratch/stefan/7787258/working/building/REAL300025478349 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478349 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478349/0 /scratch/stefan/7787258/working/building/REAL300025478349 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/222 `/scratch/stefan/7787258/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C(N)=O) `REAL300025478349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478349 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 60, 60, 60, 60, 60, 1, 11, 20, 20, 21, 29, 29, 42, 42, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 60, 1, 1, 21, 21, 29, 87, 42, 42] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 360 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: REAL300025478349 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [154, 129, 60, 60, 60, 60, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 60, 154, 195, 195, 195, 201, 201, 201, 201, 154, 154, 154, 129, 129, 60, 60, 60, 60, 60, 37, 37, 1, 60, 60, 195, 195, 201, 603, 201, 201] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478349 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478349 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478349/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478349 Building REAL300025478350 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478350' /scratch/stefan/7787258/working/building/REAL300025478350 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478350 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478350/0 /scratch/stefan/7787258/working/building/REAL300025478350 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/223 `/scratch/stefan/7787258/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478350 none CCC(C)=C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 18, 18, 12, 18, 11, 12, 6, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 20, 46, 46, 46, 46, 46, 1, 33, 33, 33, 33, 33, 18, 18, 18, 18, 18, 18, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 11, 11, 46, 1, 1] 201 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478350 none CCC(C)=C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 138, 138, 138, 101, 138, 101, 101, 93, 101, 46, 46, 46, 46, 36, 30, 36, 12, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 138, 101, 101, 101, 93, 93, 46, 46, 46, 46, 46, 30, 30, 1, 46, 46] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 918 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478350 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478350 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478350/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478350 Building REAL300025478351 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478351' /scratch/stefan/7787258/working/building/REAL300025478351 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478351 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478351/0 /scratch/stefan/7787258/working/building/REAL300025478351 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/224 `/scratch/stefan/7787258/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478351 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 3, 3, 5, 5, 12, 22, 22, 22, 22, 37, 37, 71, 102, 201, 201, 201, 201, 201, 22, 1, 1, 1, 4, 4, 4, 5, 5, 5, 12, 12, 22, 22, 22, 22, 22, 71, 71, 201, 22, 22, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478351 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 125, 130, 109, 125, 54, 54, 54, 54, 40, 36, 40, 12, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 201, 125, 125, 125, 109, 109, 54, 54, 54, 54, 54, 36, 36, 1, 54, 54, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 779 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478351 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 9, 14, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 54, 54, 54, 54, 54, 1, 22, 22, 22, 23, 23, 23, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 54, 1, 1, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478351 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478351 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478351/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478351 Building REAL300025478352 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478352' /scratch/stefan/7787258/working/building/REAL300025478352 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478352 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478352/0 /scratch/stefan/7787258/working/building/REAL300025478352 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/225 `/scratch/stefan/7787258/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)O) `REAL300025478352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478352 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 36, 36, 36, 36, 36, 1, 10, 15, 15, 17, 17, 27, 27, 27, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 6, 6, 36, 1, 1, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 81] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478352 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [111, 90, 36, 36, 36, 36, 25, 23, 25, 11, 1, 1, 1, 1, 1, 1, 1, 36, 111, 128, 128, 134, 134, 201, 201, 201, 111, 111, 111, 90, 90, 36, 36, 36, 36, 36, 23, 23, 1, 36, 36, 134, 134, 134, 134, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478352 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478352 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478352/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478352 Building REAL300025478353 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478353' /scratch/stefan/7787258/working/building/REAL300025478353 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478353 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478353/0 /scratch/stefan/7787258/working/building/REAL300025478353 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/226 `/scratch/stefan/7787258/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(CO)C(C)(C)C) `REAL300025478353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478353 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(CO)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 70, 70, 70, 70, 70, 1, 15, 19, 19, 24, 33, 24, 24, 24, 24, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 12, 12, 70, 1, 1, 24, 33, 33, 99, 24, 24, 24, 24, 24, 24, 24, 24, 24] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 350 number of broken/clashed sets: 586 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478353 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(CO)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [184, 151, 70, 70, 70, 70, 48, 41, 48, 12, 1, 1, 1, 1, 1, 1, 1, 70, 184, 192, 192, 201, 201, 201, 201, 201, 201, 184, 184, 184, 151, 151, 70, 70, 70, 70, 70, 41, 41, 1, 70, 70, 201, 201, 201, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 1386 number of broken/clashed sets: 586 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478353 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478353 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478353/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478353 Building REAL300025478354 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478354' /scratch/stefan/7787258/working/building/REAL300025478354 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478354 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478354/0 /scratch/stefan/7787258/working/building/REAL300025478354 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/227 `/scratch/stefan/7787258/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)C=CN1) `REAL300025478354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478354 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 68, 68, 68, 68, 68, 1, 13, 30, 30, 45, 45, 45, 45, 45, 45, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 68, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 235 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: REAL300025478354 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 35, 45, 45, 45, 45, 68, 68, 112, 139, 201, 201, 201, 201, 201, 45, 1, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 35, 35, 45, 45, 45, 45, 45, 112, 112, 201, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 618 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: REAL300025478354 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 121, 68, 68, 68, 68, 58, 47, 58, 13, 1, 1, 1, 1, 1, 1, 1, 68, 158, 190, 190, 201, 201, 201, 201, 201, 201, 158, 158, 158, 121, 121, 68, 68, 68, 68, 68, 47, 47, 1, 68, 68, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 750 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478354 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478354 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478354/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478354 Building REAL300025478355 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478355' /scratch/stefan/7787258/working/building/REAL300025478355 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478355 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478355/0 /scratch/stefan/7787258/working/building/REAL300025478355 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/228 `/scratch/stefan/7787258/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(=O)NC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478355 none CC1CC(=O)NC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 10, 19, 19, 19, 19, 40, 40, 77, 107, 201, 201, 201, 201, 201, 19, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 19, 19, 19, 19, 19, 77, 77, 201, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478355 none CC1CC(=O)NC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 190, 201, 167, 190, 83, 83, 83, 83, 54, 45, 54, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 167, 167, 83, 83, 83, 83, 83, 45, 45, 1, 83, 83] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 757 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478355 none CC1CC(=O)NC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 14, 19, 6, 14, 1, 1, 1, 1, 1, 1, 6, 6, 17, 26, 83, 83, 83, 83, 83, 1, 19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 17, 17, 83, 1, 1] 201 rigid atoms, others: [48, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 49, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478355 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478355 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478355/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478355 Building REAL300025478356 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478356' /scratch/stefan/7787258/working/building/REAL300025478356 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478356 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478356/0 /scratch/stefan/7787258/working/building/REAL300025478356 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/229 `/scratch/stefan/7787258/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CSN=C1) `REAL300025478356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478356 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 38, 38, 38, 38, 38, 1, 10, 25, 25, 37, 37, 37, 37, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41]) total number of confs: 162 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: REAL300025478356 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 29, 37, 37, 37, 37, 47, 47, 65, 96, 201, 201, 201, 201, 201, 37, 1, 8, 1, 1, 1, 1, 1, 14, 14, 14, 29, 29, 37, 37, 37, 37, 37, 65, 65, 201, 37, 37, 1, 1] 201 rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 517 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: REAL300025478356 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 76, 38, 38, 38, 38, 27, 24, 27, 11, 1, 1, 1, 1, 1, 1, 1, 38, 102, 173, 173, 201, 201, 201, 201, 102, 102, 102, 76, 76, 38, 38, 38, 38, 38, 24, 24, 1, 38, 38, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 667 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478356 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478356 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478356/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478356 Building REAL300025478357 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478357' /scratch/stefan/7787258/working/building/REAL300025478357 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478357 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478357/0 /scratch/stefan/7787258/working/building/REAL300025478357 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/230 `/scratch/stefan/7787258/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1) `REAL300025478357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478357 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 4, 4, 5, 5, 11, 19, 19, 19, 19, 24, 24, 37, 56, 125, 125, 125, 125, 125, 19, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 19, 19, 19, 19, 19, 37, 37, 125, 19, 19, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 48, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478357 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 120, 120, 120, 99, 120, 46, 46, 46, 46, 33, 27, 33, 13, 1, 1, 1, 1, 1, 1, 1, 46, 125, 125, 201, 201, 201, 201, 201, 120, 120, 120, 99, 99, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 125, 125] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 912 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478357 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 19, 19, 19, 11, 10, 11, 5, 10, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 46, 46, 46, 46, 46, 1, 19, 19, 37, 37, 37, 37, 37, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 7, 7, 46, 1, 1, 19, 19] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478357 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478357/1 /scratch/stefan/7787258/working/building/REAL300025478357 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/231 `/scratch/stefan/7787258/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1) `REAL300025478357.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478357 none CCC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 17, 17, 17, 17, 26, 26, 47, 57, 97, 97, 97, 97, 97, 17, 1, 7, 7, 7, 7, 7, 1, 7, 7, 7, 13, 13, 17, 17, 17, 17, 17, 47, 47, 97, 17, 17, 1] 152 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 288 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: REAL300025478357 none CCC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 97, 97, 97, 97, 89, 89, 89, 77, 89, 60, 60, 60, 60, 55, 43, 55, 13, 1, 1, 1, 1, 1, 1, 1, 60, 97, 152, 152, 152, 152, 152, 97, 89, 89, 89, 77, 77, 60, 60, 60, 60, 60, 43, 43, 1, 60, 60, 97] 152 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 687 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: REAL300025478357 none CCC1=NC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [38, 17, 17, 17, 17, 9, 8, 9, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 14, 18, 60, 60, 60, 60, 60, 1, 17, 38, 38, 38, 38, 38, 17, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 14, 14, 60, 1, 1, 17] 152 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48]) total number of confs: 259 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478357 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478357 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478357/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478357/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478357 Building REAL300025478358 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478358' /scratch/stefan/7787258/working/building/REAL300025478358 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478358 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478358/0 /scratch/stefan/7787258/working/building/REAL300025478358 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/232 `/scratch/stefan/7787258/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1) `REAL300025478358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478358 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 20, 20, 20, 20, 29, 29, 42, 64, 134, 134, 134, 134, 134, 20, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 20, 20, 20, 20, 20, 42, 42, 134, 20, 20, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478358 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 112, 112, 112, 106, 112, 61, 61, 61, 61, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 61, 134, 134, 201, 201, 201, 201, 201, 112, 112, 112, 106, 106, 61, 61, 61, 61, 61, 35, 35, 1, 61, 61, 134] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 865 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478358 none CCC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 20, 20, 20, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 61, 61, 61, 61, 61, 1, 20, 20, 39, 39, 39, 39, 39, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 9, 9, 61, 1, 1, 20] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478358 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478358/1 /scratch/stefan/7787258/working/building/REAL300025478358 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/233 `/scratch/stefan/7787258/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478358.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478358 none CCC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 12, 12, 12, 12, 20, 20, 41, 57, 119, 119, 119, 119, 119, 12, 1, 8, 8, 8, 7, 7, 1, 4, 4, 4, 8, 8, 12, 12, 12, 12, 12, 41, 41, 119, 12, 12] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478358 none CCC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 119, 119, 119, 118, 118, 118, 100, 118, 55, 55, 55, 55, 42, 34, 42, 12, 1, 1, 1, 1, 1, 1, 1, 55, 119, 201, 201, 201, 201, 201, 119, 118, 118, 118, 100, 100, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 955 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478358 none CCC1=NNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 11, 17, 55, 55, 55, 55, 55, 1, 12, 30, 30, 30, 30, 30, 12, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 11, 11, 55, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478358 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478358 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478358/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478358/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478358 Building REAL300025478359 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478359' /scratch/stefan/7787258/working/building/REAL300025478359 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478359 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478359/0 /scratch/stefan/7787258/working/building/REAL300025478359 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/234 `/scratch/stefan/7787258/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCOC1) `REAL300025478359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478359 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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: [15, 7, 1, 1, 1, 1, 1, 1, 6, 6, 16, 23, 68, 68, 68, 68, 68, 1, 15, 30, 30, 34, 35, 35, 35, 35, 35, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 16, 16, 68, 1, 1, 34, 34, 105, 35, 35, 35, 35, 35, 35] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 355 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: REAL300025478359 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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: [14, 5, 14, 24, 35, 35, 35, 35, 57, 57, 100, 126, 201, 201, 201, 201, 201, 35, 3, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 24, 35, 35, 35, 35, 35, 100, 100, 201, 35, 35, 3, 3, 6, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [45, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 563 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: REAL300025478359 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 3, 7, 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: [165, 146, 68, 68, 68, 68, 52, 41, 52, 13, 1, 1, 1, 1, 1, 1, 1, 68, 165, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 146, 146, 68, 68, 68, 68, 68, 41, 41, 1, 68, 68, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 1370 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478359 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478359 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478359/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478359 Building REAL300025478360 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478360' /scratch/stefan/7787258/working/building/REAL300025478360 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478360 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478360/0 /scratch/stefan/7787258/working/building/REAL300025478360 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/235 `/scratch/stefan/7787258/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478360 none CC1CC(C)(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 16, 32, 32, 32, 32, 44, 44, 71, 112, 201, 201, 201, 201, 201, 32, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 16, 16, 32, 32, 32, 32, 32, 71, 71, 201, 32, 32, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 50, 51, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 545 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478360 none CC1CC(C)(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 162, 201, 136, 162, 56, 56, 56, 56, 38, 28, 38, 12, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 136, 136, 56, 56, 56, 56, 56, 28, 28, 1, 56, 56, 201, 201] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 781 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478360 none CC1CC(C)(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 15, 32, 6, 15, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 56, 56, 56, 56, 56, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 6, 6, 56, 1, 1, 32, 32] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51]) total number of confs: 186 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478360 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478360 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478360/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478360 Building REAL300025478361 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478361' /scratch/stefan/7787258/working/building/REAL300025478361 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478361 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478361/0 /scratch/stefan/7787258/working/building/REAL300025478361 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/236 `/scratch/stefan/7787258/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=NN1C) `REAL300025478361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478361 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 69, 69, 69, 69, 69, 1, 12, 20, 20, 34, 35, 35, 35, 35, 35, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 69, 1, 1, 34, 34, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 263 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: REAL300025478361 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 20, 29, 35, 35, 35, 35, 51, 51, 97, 123, 201, 201, 201, 201, 201, 35, 3, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 29, 29, 35, 35, 35, 35, 35, 97, 97, 201, 35, 35, 3, 3, 1, 2, 2, 2] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 565 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: REAL300025478361 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NC=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 134, 69, 69, 69, 69, 53, 43, 53, 13, 1, 1, 1, 1, 1, 1, 1, 69, 153, 191, 191, 200, 201, 201, 201, 201, 201, 153, 153, 153, 134, 134, 69, 69, 69, 69, 69, 43, 43, 1, 69, 69, 200, 200, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 805 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478361 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478361 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478361/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478361 Building REAL300025478362 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478362' /scratch/stefan/7787258/working/building/REAL300025478362 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478362 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478362/0 /scratch/stefan/7787258/working/building/REAL300025478362 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/237 `/scratch/stefan/7787258/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478362 none CNC(=O)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 34, 28, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 39, 39, 39, 39, 39, 1, 34, 34, 34, 34, 30, 30, 28, 28, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 6, 6, 39, 1, 1] 201 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478362 none CNC(=O)CCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 140, 140, 140, 98, 140, 39, 39, 39, 39, 25, 22, 25, 11, 1, 1, 1, 1, 1, 1, 1, 39, 201, 201, 201, 201, 201, 201, 199, 199, 140, 140, 140, 98, 98, 39, 39, 39, 39, 39, 22, 22, 1, 39, 39] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 872 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478362 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478362 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478362/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478362 Building REAL300025478363 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478363' /scratch/stefan/7787258/working/building/REAL300025478363 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478363 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478363/0 /scratch/stefan/7787258/working/building/REAL300025478363 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/238 `/scratch/stefan/7787258/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1=CON=C1) `REAL300025478363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478363 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 33, 33, 33, 33, 33, 1, 11, 19, 19, 19, 19, 35, 35, 35, 35, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 33, 1, 1, 19, 19, 19, 19, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478363 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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, 9, 11, 25, 35, 35, 35, 35, 49, 49, 77, 108, 201, 201, 201, 201, 201, 35, 5, 9, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 35, 35, 35, 35, 35, 77, 77, 201, 35, 35, 5, 5, 3, 3, 1, 1] 201 rigid atoms, others: [46, 47, 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]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478363 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 77, 33, 33, 33, 33, 24, 20, 24, 11, 1, 1, 1, 1, 1, 1, 1, 33, 91, 110, 110, 110, 110, 201, 201, 201, 201, 91, 91, 91, 77, 77, 33, 33, 33, 33, 33, 20, 20, 1, 33, 33, 110, 110, 110, 110, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478363 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478363 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478363/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478363 Building REAL300025478364 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478364' /scratch/stefan/7787258/working/building/REAL300025478364 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478364 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478364/0 /scratch/stefan/7787258/working/building/REAL300025478364 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/239 `/scratch/stefan/7787258/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=C1) `REAL300025478364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478364 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 9, 12, 38, 38, 38, 38, 38, 1, 13, 26, 26, 32, 51, 51, 51, 51, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 9, 9, 38, 1, 1, 32, 32, 51, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 224 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: REAL300025478364 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 17, 37, 51, 51, 51, 51, 62, 62, 116, 139, 201, 201, 201, 201, 201, 51, 2, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 37, 37, 51, 51, 51, 51, 51, 116, 116, 201, 51, 51, 2, 2, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 648 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: REAL300025478364 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CSN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 14, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 81, 38, 38, 38, 38, 35, 30, 35, 13, 1, 1, 1, 1, 1, 1, 1, 38, 99, 126, 126, 130, 201, 201, 201, 201, 99, 99, 99, 81, 81, 38, 38, 38, 38, 38, 30, 30, 1, 38, 38, 130, 130, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 650 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478364 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478364 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478364/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478364 Building REAL300025478365 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478365' /scratch/stefan/7787258/working/building/REAL300025478365 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478365 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478365/0 /scratch/stefan/7787258/working/building/REAL300025478365 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/240 `/scratch/stefan/7787258/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478365 none C=CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 5, 5, 5, 5, 5, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 5, 1, 1, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52, 53, 54]) total number of confs: 24 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: REAL300025478365 none C=CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 11 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478365 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478365 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478365/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478365 Building REAL300025478366 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478366' /scratch/stefan/7787258/working/building/REAL300025478366 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478366 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478366/0 /scratch/stefan/7787258/working/building/REAL300025478366 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/241 `/scratch/stefan/7787258/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCF) `REAL300025478366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478366 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 53, 53, 53, 53, 53, 1, 12, 22, 22, 23, 24, 24, 39, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1, 23, 23, 24, 24, 24, 24, 39, 39] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478366 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 118, 53, 53, 53, 53, 37, 29, 37, 13, 1, 1, 1, 1, 1, 1, 1, 53, 163, 198, 198, 200, 201, 201, 201, 163, 163, 163, 118, 118, 53, 53, 53, 53, 53, 29, 29, 1, 53, 53, 200, 200, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478366 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478366 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478366/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478366 Building REAL300025478367 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478367' /scratch/stefan/7787258/working/building/REAL300025478367 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478367 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478367/0 /scratch/stefan/7787258/working/building/REAL300025478367 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/242 `/scratch/stefan/7787258/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCO) `REAL300025478367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478367 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 78, 78, 78, 78, 78, 1, 9, 18, 18, 28, 28, 35, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 13, 13, 78, 1, 1, 28, 28, 35, 35, 105] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 377 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478367 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [165, 145, 78, 78, 78, 78, 56, 44, 56, 13, 1, 1, 1, 1, 1, 1, 1, 78, 165, 174, 174, 201, 201, 201, 165, 165, 165, 145, 145, 78, 78, 78, 78, 78, 44, 44, 1, 78, 78, 201, 201, 201, 201, 603] 603 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1402 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478367 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478367 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478367/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478367 Building REAL300025478368 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478368' /scratch/stefan/7787258/working/building/REAL300025478368 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478368 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478368/0 /scratch/stefan/7787258/working/building/REAL300025478368 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/243 `/scratch/stefan/7787258/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CCCO1) `REAL300025478368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478368 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 3, 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: [14, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 81, 81, 81, 81, 81, 1, 14, 18, 18, 18, 30, 18, 18, 18, 18, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 13, 13, 81, 1, 1, 30, 30, 90, 18, 18, 18, 18, 18, 18] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 349 number of broken/clashed sets: 212 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478368 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 3, 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: [5, 3, 5, 11, 18, 18, 18, 18, 32, 32, 64, 96, 201, 201, 201, 201, 201, 18, 1, 3, 1, 1, 6, 1, 1, 1, 1, 5, 5, 5, 11, 11, 18, 18, 18, 18, 18, 64, 64, 201, 18, 18, 6, 6, 18, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 20, 21, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 508 number of broken/clashed sets: 212 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478368 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 3, 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: [189, 172, 81, 81, 81, 81, 56, 43, 56, 13, 1, 1, 1, 1, 1, 1, 1, 81, 189, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 172, 172, 81, 81, 81, 81, 81, 43, 43, 1, 81, 81, 201, 201, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 1371 number of broken/clashed sets: 212 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478368 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478368 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478368/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478368 Building REAL300025478369 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478369' /scratch/stefan/7787258/working/building/REAL300025478369 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478369 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478369/0 /scratch/stefan/7787258/working/building/REAL300025478369 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/244 `/scratch/stefan/7787258/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478369 none CCC(C)CC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 40, 41, 26, 12, 26, 11, 12, 6, 11, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 59, 59, 59, 59, 59, 1, 43, 43, 43, 43, 43, 41, 41, 41, 41, 40, 40, 26, 26, 26, 26, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 13, 13, 59, 1, 1] 201 rigid atoms, others: [16, 11, 12, 13, 14, 47, 48, 49, 50, 51, 55, 56, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 52, 53, 54]) total number of confs: 298 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: REAL300025478369 none CCC(C)CC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 176, 116, 176, 115, 116, 109, 115, 59, 59, 59, 59, 44, 36, 44, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 115, 115, 115, 109, 109, 59, 59, 59, 59, 59, 36, 36, 1, 59, 59] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 899 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478369 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478369 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478369/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478369 Building REAL300025478370 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478370' /scratch/stefan/7787258/working/building/REAL300025478370 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478370 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478370/0 /scratch/stefan/7787258/working/building/REAL300025478370 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/245 `/scratch/stefan/7787258/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)N1C=CC=N1) `REAL300025478370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478370 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 53, 53, 53, 53, 53, 1, 11, 27, 27, 36, 36, 44, 44, 44, 44, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 53, 1, 1, 36, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 256 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: REAL300025478370 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 37, 44, 44, 44, 44, 65, 65, 101, 124, 201, 201, 201, 201, 201, 44, 6, 15, 1, 6, 1, 1, 1, 1, 1, 22, 22, 22, 37, 37, 44, 44, 44, 44, 44, 101, 101, 201, 44, 44, 6, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 20, 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, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 583 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: REAL300025478370 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 108, 53, 53, 53, 53, 39, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 53, 121, 179, 179, 196, 196, 201, 201, 201, 201, 121, 121, 121, 108, 108, 53, 53, 53, 53, 53, 33, 33, 1, 53, 53, 196, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 759 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478370 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478370 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478370/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478370 Building REAL300025478371 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478371' /scratch/stefan/7787258/working/building/REAL300025478371 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478371 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478371/0 /scratch/stefan/7787258/working/building/REAL300025478371 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/246 `/scratch/stefan/7787258/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CO1) `REAL300025478371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478371 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 54, 54, 54, 54, 54, 1, 12, 22, 22, 36, 45, 45, 45, 45, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 54, 1, 1, 36, 36, 45, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 261 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478371 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 21, 37, 45, 45, 45, 45, 58, 58, 108, 129, 201, 201, 201, 201, 201, 45, 4, 13, 1, 1, 1, 1, 1, 1, 21, 21, 21, 37, 37, 45, 45, 45, 45, 45, 108, 108, 201, 45, 45, 4, 4, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 606 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478371 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 103, 54, 54, 54, 54, 40, 31, 40, 12, 1, 1, 1, 1, 1, 1, 1, 54, 116, 144, 144, 174, 201, 201, 201, 201, 116, 116, 116, 103, 103, 54, 54, 54, 54, 54, 31, 31, 1, 54, 54, 174, 174, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 781 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478371 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478371 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478371/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478371 Building REAL300025478372 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478372' /scratch/stefan/7787258/working/building/REAL300025478372 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478372 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478372/0 /scratch/stefan/7787258/working/building/REAL300025478372 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/247 `/scratch/stefan/7787258/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[C@@H]1CC=CCC1) `REAL300025478372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478372 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 5, 10, 15, 38, 38, 38, 38, 38, 1, 12, 21, 21, 25, 38, 38, 38, 38, 38, 38, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 38, 1, 1, 25, 25, 38, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478372 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 13, 29, 38, 38, 38, 38, 52, 52, 105, 126, 201, 201, 201, 201, 201, 38, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 29, 29, 38, 38, 38, 38, 38, 105, 105, 201, 38, 38, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478372 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 79, 38, 38, 38, 38, 30, 28, 30, 11, 1, 1, 1, 1, 1, 1, 1, 38, 94, 113, 113, 132, 201, 201, 201, 201, 201, 201, 94, 94, 94, 79, 79, 38, 38, 38, 38, 38, 28, 28, 1, 38, 38, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478372 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478372 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478372/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478372 Building REAL300025478373 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478373' /scratch/stefan/7787258/working/building/REAL300025478373 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478373 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478373/0 /scratch/stefan/7787258/working/building/REAL300025478373 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/248 `/scratch/stefan/7787258/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC2CC2C1) `REAL300025478373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 15, 15, 15, 15, 15, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 7, 7, 15, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11] 22 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) 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: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 10, 11, 11, 11, 11, 14, 14, 20, 20, 22, 22, 22, 22, 22, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 11, 11, 11, 11, 11, 20, 20, 22, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C[NH+]1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 15, 15, 15, 15, 14, 13, 14, 10, 1, 1, 1, 1, 1, 1, 1, 15, 18, 18, 18, 18, 22, 22, 22, 22, 22, 22, 18, 18, 18, 18, 18, 15, 15, 15, 15, 15, 13, 13, 1, 15, 15, 18, 18, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478373 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478373/1 /scratch/stefan/7787258/working/building/REAL300025478373 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/249 `/scratch/stefan/7787258/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC2CC2C1) `REAL300025478373.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 13, 21, 65, 65, 65, 65, 65, 1, 13, 25, 25, 33, 37, 37, 37, 37, 37, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 65, 1, 1, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 251 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: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 28, 37, 37, 37, 37, 46, 46, 90, 113, 201, 201, 201, 201, 201, 37, 5, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 28, 28, 37, 37, 37, 37, 37, 90, 90, 201, 37, 37, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 552 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: REAL300025478373 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 135, 65, 65, 65, 65, 46, 34, 46, 12, 1, 1, 1, 1, 1, 1, 1, 65, 162, 189, 189, 201, 201, 201, 201, 201, 201, 162, 162, 162, 135, 135, 65, 65, 65, 65, 65, 34, 34, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 800 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478373 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478373 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478373/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478373/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478373 Building REAL300025478374 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478374' /scratch/stefan/7787258/working/building/REAL300025478374 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478374 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478374/0 /scratch/stefan/7787258/working/building/REAL300025478374 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/250 `/scratch/stefan/7787258/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2CC2C1) `REAL300025478374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478374 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 16, 48, 48, 48, 48, 48, 1, 13, 20, 20, 24, 43, 43, 43, 43, 43, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 48, 1, 1, 24, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478374 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 17, 33, 43, 43, 43, 43, 58, 58, 111, 129, 201, 201, 201, 201, 201, 43, 5, 10, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 43, 43, 43, 43, 43, 111, 111, 201, 43, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 612 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478374 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 91, 48, 48, 48, 48, 38, 32, 38, 13, 1, 1, 1, 1, 1, 1, 1, 48, 112, 128, 128, 147, 201, 201, 201, 201, 201, 112, 112, 112, 91, 91, 48, 48, 48, 48, 48, 32, 32, 1, 48, 48, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478374 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478374 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478374/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478374 Building REAL300025478375 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478375' /scratch/stefan/7787258/working/building/REAL300025478375 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478375 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478375/0 /scratch/stefan/7787258/working/building/REAL300025478375 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/251 `/scratch/stefan/7787258/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(CF)=C1) `REAL300025478375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478375 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(CF)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 1, 5, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 72, 72, 72, 72, 72, 1, 11, 23, 23, 24, 24, 24, 24, 46, 24, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 15, 72, 1, 1, 46, 46, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478375 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(CF)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 1, 5, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 17, 24, 24, 24, 24, 42, 42, 76, 108, 201, 201, 201, 201, 201, 24, 1, 5, 1, 1, 1, 1, 1, 8, 1, 9, 9, 9, 17, 17, 24, 24, 24, 24, 24, 76, 76, 201, 24, 24, 8, 8, 1] 201 rigid atoms, others: [44, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478375 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(CF)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 1, 5, 15, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 129, 72, 72, 72, 72, 51, 41, 51, 13, 1, 1, 1, 1, 1, 1, 1, 72, 160, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 129, 129, 72, 72, 72, 72, 72, 41, 41, 1, 72, 72, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478375 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478375 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478375/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478375 Building REAL300025478376 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478376' /scratch/stefan/7787258/working/building/REAL300025478376 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478376 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478376/0 /scratch/stefan/7787258/working/building/REAL300025478376 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/252 `/scratch/stefan/7787258/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(F)=N1) `REAL300025478376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478376 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 6, 6, 13, 21, 70, 70, 70, 70, 70, 1, 16, 30, 30, 37, 37, 37, 37, 37, 37, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 13, 13, 70, 1, 1, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478376 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 25, 37, 37, 37, 37, 50, 50, 83, 115, 201, 201, 201, 201, 201, 37, 1, 7, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 25, 25, 37, 37, 37, 37, 37, 83, 83, 201, 37, 37, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 540 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478376 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 15, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 136, 70, 70, 70, 70, 50, 40, 50, 13, 1, 1, 1, 1, 1, 1, 1, 70, 168, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 136, 136, 70, 70, 70, 70, 70, 40, 40, 1, 70, 70, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 770 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478376 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478376 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478376/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478376 Building REAL300025478377 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478377' /scratch/stefan/7787258/working/building/REAL300025478377 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478377 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478377/0 /scratch/stefan/7787258/working/building/REAL300025478377 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/253 `/scratch/stefan/7787258/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478377 none COC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 19, 19, 19, 19, 12, 19, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 57, 57, 57, 57, 57, 1, 22, 22, 22, 19, 19, 19, 19, 19, 19, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 12, 12, 57, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478377 none COC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 201, 117, 142, 57, 57, 57, 57, 41, 33, 41, 12, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 117, 117, 57, 57, 57, 57, 57, 33, 33, 1, 57, 57] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 774 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478377 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478377 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478377/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478377 Building REAL300025478378 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478378' /scratch/stefan/7787258/working/building/REAL300025478378 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478378 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478378/0 /scratch/stefan/7787258/working/building/REAL300025478378 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/254 `/scratch/stefan/7787258/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478378 none CCCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 6, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 20, 20, 20, 20, 20, 1, 6, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 6, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 5, 5, 20, 1, 1, 10, 10, 10, 10, 10, 10] 21 rigid atoms, others: [43, 8, 9, 10, 11, 12, 45, 44, 50, 49, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52, 53, 54, 55, 56]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478378 none CCCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 17, 20, 10, 1, 1, 1, 1, 1, 1, 1, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 17, 17, 1, 20, 20, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [48, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478378 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478378 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478378/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478378 Building REAL300025478379 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478379' /scratch/stefan/7787258/working/building/REAL300025478379 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478379 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478379/0 /scratch/stefan/7787258/working/building/REAL300025478379 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/255 `/scratch/stefan/7787258/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478379 none CC1=CN=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 27, 42, 42, 42, 42, 53, 53, 95, 122, 201, 201, 201, 201, 201, 42, 1, 2, 2, 2, 1, 1, 14, 14, 14, 27, 27, 42, 42, 42, 42, 42, 95, 95, 201, 42, 42] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478379 none CC1=CN=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 157, 146, 157, 124, 146, 66, 66, 66, 66, 55, 42, 55, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 146, 146, 146, 124, 124, 66, 66, 66, 66, 66, 42, 42, 1, 66, 66] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478379 none CC1=CN=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 42, 21, 14, 21, 6, 14, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 66, 66, 66, 66, 66, 1, 42, 42, 42, 42, 42, 42, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 10, 10, 66, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478379 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478379 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478379/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478379 Building REAL300025478380 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478380' /scratch/stefan/7787258/working/building/REAL300025478380 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478380 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478380/0 /scratch/stefan/7787258/working/building/REAL300025478380 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/256 `/scratch/stefan/7787258/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)[NH+](C)C) `REAL300025478380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478380 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 8, 8, 8, 8, 8, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 6, 6, 8, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 49 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478380 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 8, 8, 8, 8, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 8, 8, 8, 8, 8, 7, 7, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 45 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478380 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478380 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478380/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478380 Building REAL300025478381 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478381' /scratch/stefan/7787258/working/building/REAL300025478381 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478381 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478381/0 /scratch/stefan/7787258/working/building/REAL300025478381 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/257 `/scratch/stefan/7787258/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)CO) `REAL300025478381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478381 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 15, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 63, 63, 63, 63, 63, 1, 11, 19, 19, 19, 19, 19, 23, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 63, 1, 1, 23, 23, 69] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478381 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)CO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 15, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 142, 63, 63, 63, 63, 46, 39, 46, 12, 1, 1, 1, 1, 1, 1, 1, 63, 174, 201, 201, 201, 201, 201, 201, 174, 174, 174, 142, 142, 63, 63, 63, 63, 63, 39, 39, 1, 63, 63, 201, 201, 603] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 1383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478381 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478381 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478381/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478381 Building REAL300025478382 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478382' /scratch/stefan/7787258/working/building/REAL300025478382 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478382 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478382/0 /scratch/stefan/7787258/working/building/REAL300025478382 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/258 `/scratch/stefan/7787258/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCO) `REAL300025478382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478382 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 46, 46, 46, 46, 46, 1, 13, 25, 25, 28, 28, 28, 37, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1, 28, 28, 28, 28, 28, 28, 37, 37, 111] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478382 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [150, 107, 46, 46, 46, 46, 32, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 46, 150, 198, 198, 201, 201, 201, 201, 150, 150, 150, 107, 107, 46, 46, 46, 46, 46, 25, 25, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478382 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478382 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478382/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478382 Building REAL300025478383 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478383' /scratch/stefan/7787258/working/building/REAL300025478383 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478383 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478383/0 /scratch/stefan/7787258/working/building/REAL300025478383 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/259 `/scratch/stefan/7787258/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1) `REAL300025478383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478383 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 12, 12, 28, 43, 43, 43, 43, 65, 65, 106, 132, 201, 201, 201, 201, 201, 43, 1, 1, 1, 2, 2, 2, 12, 12, 12, 28, 28, 43, 43, 43, 43, 43, 106, 106, 201, 43, 43, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 588 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: REAL300025478383 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 126, 138, 114, 126, 59, 59, 59, 59, 47, 37, 47, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 126, 126, 126, 114, 114, 59, 59, 59, 59, 59, 37, 37, 1, 59, 59, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 653 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: REAL300025478383 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 20, 13, 20, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 59, 59, 59, 59, 59, 1, 43, 43, 43, 43, 43, 43, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 59, 1, 1, 43] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44]) total number of confs: 202 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478383 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478383 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478383/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478383 Building REAL300025478384 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478384' /scratch/stefan/7787258/working/building/REAL300025478384 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478384 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478384/0 /scratch/stefan/7787258/working/building/REAL300025478384 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/260 `/scratch/stefan/7787258/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478384 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 25, 40, 40, 40, 40, 52, 52, 91, 116, 201, 201, 201, 201, 201, 40, 1, 2, 2, 2, 1, 1, 12, 12, 12, 25, 25, 40, 40, 40, 40, 40, 91, 91, 201, 40, 40, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478384 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 155, 166, 127, 155, 62, 62, 62, 62, 48, 40, 48, 12, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 155, 155, 155, 127, 127, 62, 62, 62, 62, 62, 40, 40, 1, 62, 62, 201] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 706 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478384 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 24, 13, 24, 6, 13, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 62, 62, 62, 62, 62, 1, 40, 40, 40, 40, 40, 40, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 11, 11, 62, 1, 1, 40] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478384 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478384 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478384/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478384 Building REAL300025478385 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478385' /scratch/stefan/7787258/working/building/REAL300025478385 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478385 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478385/0 /scratch/stefan/7787258/working/building/REAL300025478385 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/261 `/scratch/stefan/7787258/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CNC(=O)C1) `REAL300025478385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478385 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 6, 7, 14, 22, 66, 66, 66, 66, 66, 1, 14, 26, 26, 37, 37, 37, 37, 37, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 14, 66, 1, 1, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478385 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 26, 37, 37, 37, 37, 57, 57, 107, 126, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 37, 37, 37, 37, 37, 107, 107, 201, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 596 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478385 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 117, 66, 66, 66, 66, 47, 37, 47, 13, 1, 1, 1, 1, 1, 1, 1, 66, 148, 184, 184, 201, 201, 201, 201, 201, 148, 148, 148, 117, 117, 66, 66, 66, 66, 66, 37, 37, 1, 66, 66, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 762 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478385 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478385 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478385/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478385 Building REAL300025478386 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478386' /scratch/stefan/7787258/working/building/REAL300025478386 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478386 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478386/0 /scratch/stefan/7787258/working/building/REAL300025478386 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/262 `/scratch/stefan/7787258/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC(F)(F)F) `REAL300025478386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478386 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 15, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 48, 48, 48, 48, 48, 1, 10, 12, 12, 23, 38, 43, 43, 43, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 12, 12, 48, 1, 1, 23, 23] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478386 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 15, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 97, 48, 48, 48, 48, 42, 36, 42, 13, 1, 1, 1, 1, 1, 1, 1, 48, 106, 112, 112, 165, 201, 201, 201, 201, 106, 106, 106, 97, 97, 48, 48, 48, 48, 48, 36, 36, 1, 48, 48, 165, 165] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478386 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478386 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478386/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478386 Building REAL300025478387 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478387' /scratch/stefan/7787258/working/building/REAL300025478387 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478387 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478387/0 /scratch/stefan/7787258/working/building/REAL300025478387 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/263 `/scratch/stefan/7787258/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CNC(=O)N1) `REAL300025478387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478387 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 15, 23, 57, 57, 57, 57, 57, 1, 14, 31, 31, 46, 46, 46, 46, 46, 46, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 15, 15, 57, 1, 1, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 251 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: REAL300025478387 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 35, 46, 46, 46, 46, 76, 76, 121, 149, 201, 201, 201, 201, 201, 46, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 35, 35, 46, 46, 46, 46, 46, 121, 121, 201, 46, 46, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 629 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: REAL300025478387 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 115, 57, 57, 57, 57, 44, 38, 44, 13, 1, 1, 1, 1, 1, 1, 1, 57, 147, 179, 179, 201, 201, 201, 201, 201, 201, 147, 147, 147, 115, 115, 57, 57, 57, 57, 57, 38, 38, 1, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 764 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478387 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478387 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478387/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478387 Building REAL300025478388 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478388' /scratch/stefan/7787258/working/building/REAL300025478388 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478388 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478388/0 /scratch/stefan/7787258/working/building/REAL300025478388 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/264 `/scratch/stefan/7787258/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CS1) `REAL300025478388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478388 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 53, 53, 53, 53, 53, 1, 15, 25, 25, 51, 51, 51, 51, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 11, 11, 53, 1, 1, 51, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478388 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 17, 40, 51, 51, 51, 51, 64, 64, 109, 133, 201, 201, 201, 201, 201, 51, 1, 11, 1, 1, 1, 1, 1, 17, 17, 17, 40, 40, 51, 51, 51, 51, 51, 109, 109, 201, 51, 51, 1, 1] 201 rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 625 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478388 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 8, 1, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 110, 53, 53, 53, 53, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 53, 133, 177, 177, 201, 201, 201, 201, 133, 133, 133, 110, 110, 53, 53, 53, 53, 53, 36, 36, 1, 53, 53, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478388 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478388 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478388/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478388 Building REAL300025478389 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478389' /scratch/stefan/7787258/working/building/REAL300025478389 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478389 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478389/0 /scratch/stefan/7787258/working/building/REAL300025478389 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/265 `/scratch/stefan/7787258/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1) `REAL300025478389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478389 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 31, 48, 48, 48, 48, 66, 66, 110, 130, 201, 201, 201, 201, 201, 48, 1, 2, 2, 2, 1, 1, 16, 16, 16, 31, 31, 48, 48, 48, 48, 48, 110, 110, 201, 48, 48, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 606 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: REAL300025478389 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 148, 160, 124, 148, 66, 66, 66, 66, 53, 43, 53, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 148, 148, 148, 124, 124, 66, 66, 66, 66, 66, 43, 43, 1, 66, 66, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 720 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: REAL300025478389 none CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 21, 13, 21, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 66, 66, 66, 66, 66, 1, 48, 48, 48, 48, 48, 48, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 66, 1, 1, 48] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46]) total number of confs: 217 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478389 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478389 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478389/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478389 Building REAL300025478390 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478390' /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478390 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478390/0 /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/266 `/scratch/stefan/7787258/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@@H+]1C) `REAL300025478390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 6, 1, 1, 1, 1, 1, 1, 4, 4, 11, 14, 25, 25, 25, 25, 25, 1, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 6, 6, 1, 1, 1, 1, 1, 11, 11, 25, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 29 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 3, 5, 7, 10, 10, 10, 10, 14, 14, 24, 25, 29, 29, 29, 29, 29, 10, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 24, 24, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 115 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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 25, 25, 25, 23, 20, 23, 13, 1, 1, 1, 1, 1, 1, 1, 25, 27, 27, 27, 29, 29, 29, 29, 29, 29, 29, 27, 27, 27, 27, 27, 25, 25, 25, 25, 25, 20, 20, 1, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478390/1 /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/267 `/scratch/stefan/7787258/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@H+]1C) `REAL300025478390.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 3, 4, 8, 10, 20, 20, 20, 20, 20, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 8, 8, 20, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 25 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 3, 5, 7, 9, 9, 9, 9, 11, 11, 18, 21, 25, 25, 25, 25, 25, 9, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 18, 18, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 92 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: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 20, 20, 20, 20, 19, 20, 11, 1, 1, 1, 1, 1, 1, 1, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 19, 19, 1, 20, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478390/2 /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/268 `/scratch/stefan/7787258/working/3D/268' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCCN1C) `REAL300025478390.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478390/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 66, 66, 66, 66, 66, 1, 16, 30, 30, 33, 33, 33, 33, 33, 33, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 14, 14, 66, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 220 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 21, 33, 33, 33, 33, 47, 47, 85, 115, 201, 201, 201, 201, 201, 33, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 33, 33, 33, 33, 33, 85, 85, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 543 number of broken/clashed sets: 156 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478390 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCCN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 137, 66, 66, 66, 66, 44, 36, 44, 12, 1, 1, 1, 1, 1, 1, 1, 66, 160, 200, 200, 201, 201, 201, 201, 201, 201, 160, 160, 160, 137, 137, 66, 66, 66, 66, 66, 36, 36, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 766 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478390 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478390 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478390/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478390/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478390/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478390 Building REAL300025478391 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478391' /scratch/stefan/7787258/working/building/REAL300025478391 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478391 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478391/0 /scratch/stefan/7787258/working/building/REAL300025478391 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/269 `/scratch/stefan/7787258/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CC1) `REAL300025478391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478391 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 52, 52, 52, 52, 52, 1, 9, 17, 17, 18, 29, 18, 18, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 7, 7, 52, 1, 1, 29, 29, 87, 18, 18, 18, 18] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 287 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: REAL300025478391 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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: [5, 3, 5, 12, 18, 18, 18, 18, 29, 29, 49, 86, 201, 201, 201, 201, 201, 18, 1, 3, 1, 1, 8, 1, 1, 5, 5, 5, 12, 12, 18, 18, 18, 18, 18, 49, 49, 201, 18, 18, 8, 8, 24, 1, 1, 1, 1] 603 rigid atoms, others: [43, 44, 45, 46, 18, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 518 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: REAL300025478391 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 4, 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: [130, 117, 52, 52, 52, 52, 36, 29, 36, 13, 1, 1, 1, 1, 1, 1, 1, 52, 130, 201, 201, 201, 201, 201, 201, 130, 130, 130, 117, 117, 52, 52, 52, 52, 52, 29, 29, 1, 52, 52, 201, 201, 603, 201, 201, 201, 201] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1360 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478391 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478391 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478391/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478391 Building REAL300025478392 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478392' /scratch/stefan/7787258/working/building/REAL300025478392 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478392 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478392/0 /scratch/stefan/7787258/working/building/REAL300025478392 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/270 `/scratch/stefan/7787258/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478392 none CCC1=CNC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 19, 30, 30, 30, 30, 41, 41, 68, 87, 171, 171, 171, 171, 171, 30, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 8, 19, 19, 30, 30, 30, 30, 30, 68, 68, 171, 30, 30] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 462 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: REAL300025478392 none CCC1=CNC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 171, 171, 171, 171, 125, 123, 125, 107, 123, 62, 62, 62, 62, 53, 38, 53, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 171, 171, 171, 123, 123, 123, 107, 107, 62, 62, 62, 62, 62, 38, 38, 1, 62, 62] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 760 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: REAL300025478392 none CCC1=CNC=C1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 30, 30, 30, 30, 30, 15, 12, 15, 5, 12, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 62, 62, 62, 62, 62, 1, 41, 41, 41, 41, 41, 30, 30, 30, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 62, 1, 1] 201 rigid atoms, others: [48, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 49, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478392 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478392 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478392/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478392 Building REAL300025478393 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478393' /scratch/stefan/7787258/working/building/REAL300025478393 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478393 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478393/0 /scratch/stefan/7787258/working/building/REAL300025478393 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/271 `/scratch/stefan/7787258/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCC[C@H]1CF) `REAL300025478393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478393 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCC[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 75, 75, 75, 75, 75, 1, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 31, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 75, 1, 1, 24, 24, 24, 24, 24, 24, 31, 31] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 233 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: REAL300025478393 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCC[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 16, 24, 24, 24, 24, 39, 39, 73, 99, 201, 201, 201, 201, 201, 24, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 16, 16, 24, 24, 24, 24, 24, 73, 73, 201, 24, 24, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51]) total number of confs: 520 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: REAL300025478393 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCC[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 144, 75, 75, 75, 75, 54, 43, 54, 13, 1, 1, 1, 1, 1, 1, 1, 75, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 144, 144, 75, 75, 75, 75, 75, 43, 43, 1, 75, 75, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 745 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478393 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478393 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478393/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478393 Building REAL300025478394 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478394' /scratch/stefan/7787258/working/building/REAL300025478394 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478394 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478394/0 /scratch/stefan/7787258/working/building/REAL300025478394 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/272 `/scratch/stefan/7787258/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478394 none CC(C)[C@@H](O)[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 23, 30, 30, 18, 23, 23, 14, 18, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 82, 82, 82, 82, 82, 1, 30, 30, 30, 30, 30, 30, 30, 90, 23, 23, 23, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 16, 16, 82, 1, 1] 603 rigid atoms, others: [48, 49, 47, 45, 14, 13, 16, 17, 18, 46, 54, 15, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52]) total number of confs: 359 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478394 none CC(C)[C@@H](O)[C@@H](C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 200, 201, 201, 188, 200, 169, 188, 82, 82, 82, 82, 52, 40, 52, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 188, 188, 188, 169, 169, 82, 82, 82, 82, 82, 40, 40, 1, 82, 82] 603 rigid atoms, others: [52, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 1360 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478394 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478394 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478394/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478394 Building REAL300025478395 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478395' /scratch/stefan/7787258/working/building/REAL300025478395 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478395 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478395/0 /scratch/stefan/7787258/working/building/REAL300025478395 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/273 `/scratch/stefan/7787258/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478395 none COC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 6, 14, 14, 14, 14, 29, 40, 40, 40, 40, 56, 56, 91, 123, 201, 201, 201, 201, 201, 40, 1, 1, 4, 4, 4, 6, 6, 14, 14, 14, 29, 29, 40, 40, 40, 40, 40, 91, 91, 201, 40, 40, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 46, 47, 48, 49, 24, 25] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478395 none COC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 131, 131, 131, 120, 131, 78, 78, 78, 78, 60, 43, 60, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 198, 198, 131, 131, 131, 120, 120, 78, 78, 78, 78, 78, 43, 43, 1, 78, 78, 201, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 834 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478395 none COC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 34, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 78, 78, 78, 78, 78, 1, 40, 40, 42, 42, 42, 34, 34, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 78, 1, 1, 40, 40, 40, 40] 201 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478395 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478395 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478395/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478395 Building REAL300025478396 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478396' /scratch/stefan/7787258/working/building/REAL300025478396 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478396 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478396/0 /scratch/stefan/7787258/working/building/REAL300025478396 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/274 `/scratch/stefan/7787258/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN(C)N=C1) `REAL300025478396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478396 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 5, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 73, 73, 73, 73, 73, 1, 13, 24, 24, 38, 44, 44, 44, 44, 44, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 73, 1, 1, 38, 38, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 281 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: REAL300025478396 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 5, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 23, 35, 44, 44, 44, 44, 55, 55, 93, 124, 201, 201, 201, 201, 201, 44, 5, 14, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 35, 35, 44, 44, 44, 44, 44, 93, 93, 201, 44, 44, 5, 5, 2, 2, 2, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 579 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: REAL300025478396 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=NN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 8, 8, 5, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 132, 73, 73, 73, 73, 51, 38, 51, 12, 1, 1, 1, 1, 1, 1, 1, 73, 140, 177, 177, 197, 201, 201, 201, 201, 201, 140, 140, 140, 132, 132, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73, 197, 197, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 803 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478396 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478396 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478396/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478396 Building REAL300025478397 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478397' /scratch/stefan/7787258/working/building/REAL300025478397 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478397 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478397/0 /scratch/stefan/7787258/working/building/REAL300025478397 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/275 `/scratch/stefan/7787258/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC1(F)F) `REAL300025478397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478397 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 16, 54, 54, 54, 54, 54, 1, 13, 23, 23, 25, 44, 44, 44, 44, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 54, 1, 1, 25, 25, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478397 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 34, 44, 44, 44, 44, 61, 61, 105, 125, 201, 201, 201, 201, 201, 44, 6, 11, 1, 1, 1, 1, 1, 1, 16, 16, 16, 34, 34, 44, 44, 44, 44, 44, 105, 105, 201, 44, 44, 6, 6, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478397 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 108, 54, 54, 54, 54, 46, 38, 46, 13, 1, 1, 1, 1, 1, 1, 1, 54, 133, 157, 157, 159, 201, 201, 201, 201, 133, 133, 133, 108, 108, 54, 54, 54, 54, 54, 38, 38, 1, 54, 54, 159, 159, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478397 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478397 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478397/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478397 Building REAL300025478398 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478398' /scratch/stefan/7787258/working/building/REAL300025478398 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478398 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478398/0 /scratch/stefan/7787258/working/building/REAL300025478398 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/276 `/scratch/stefan/7787258/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1) `REAL300025478398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478398 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 51, 51, 51, 51, 51, 1, 16, 22, 22, 29, 29, 29, 29, 29, 29, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 8, 8, 51, 1, 1, 29, 29, 29] 112 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478398 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 7, 12, 22, 29, 29, 29, 29, 32, 32, 58, 71, 112, 112, 112, 112, 112, 29, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 29, 29, 29, 29, 29, 58, 58, 112, 29, 29, 1, 1, 1] 112 rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 343 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478398 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 81, 51, 51, 51, 51, 47, 35, 47, 13, 1, 1, 1, 1, 1, 1, 1, 51, 103, 109, 109, 112, 112, 112, 112, 112, 112, 103, 103, 103, 81, 81, 51, 51, 51, 51, 51, 35, 35, 1, 51, 51, 112, 112, 112] 112 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478398 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478398 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478398/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478398 Building REAL300025478399 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478399' /scratch/stefan/7787258/working/building/REAL300025478399 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478399 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478399/0 /scratch/stefan/7787258/working/building/REAL300025478399 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/277 `/scratch/stefan/7787258/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478399 none CC[C@H](C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 39, 32, 39, 39, 17, 32, 32, 15, 17, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 14, 20, 59, 59, 59, 59, 59, 1, 40, 40, 40, 40, 40, 39, 39, 39, 96, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 14, 14, 59, 1, 1] 603 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 50, 51, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 376 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478399 none CC[C@H](C)[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 189, 201, 201, 134, 189, 189, 129, 134, 112, 129, 59, 59, 59, 59, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 567, 129, 129, 129, 112, 112, 59, 59, 59, 59, 59, 39, 39, 1, 59, 59] 603 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1498 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478399 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478399 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478399/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478399 Building REAL300025478400 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478400' /scratch/stefan/7787258/working/building/REAL300025478400 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478400 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478400/0 /scratch/stefan/7787258/working/building/REAL300025478400 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/278 `/scratch/stefan/7787258/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](O)C2) `REAL300025478400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478400 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 17, 41, 41, 41, 41, 41, 1, 12, 19, 19, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 41, 1, 1, 20, 20, 60, 20, 20] 249 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478400 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 14, 20, 20, 20, 20, 22, 22, 43, 49, 83, 83, 83, 83, 83, 20, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 20, 20, 20, 20, 20, 43, 43, 83, 20, 20, 1, 1, 3, 1, 1] 249 rigid atoms, others: [43, 44, 46, 47, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478400 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [71, 62, 41, 41, 41, 41, 38, 25, 38, 13, 1, 1, 1, 1, 1, 1, 1, 41, 71, 83, 83, 83, 83, 83, 83, 83, 83, 83, 71, 71, 71, 62, 62, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41, 83, 83, 249, 83, 83] 249 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478400 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478400 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478400/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478400 Building REAL300025478401 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478401' /scratch/stefan/7787258/working/building/REAL300025478401 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478401 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478401/0 /scratch/stefan/7787258/working/building/REAL300025478401 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/279 `/scratch/stefan/7787258/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478401 none CCCOCCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 23, 17, 12, 10, 8, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 82, 82, 82, 82, 82, 1, 40, 40, 40, 40, 40, 23, 23, 12, 12, 10, 10, 8, 8, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 13, 13, 82, 1, 1] 201 rigid atoms, others: [16, 15, 11, 12, 13, 14, 45, 48, 49, 46, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478401 none CCCOCCCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 184, 168, 157, 157, 124, 124, 124, 121, 124, 82, 82, 82, 82, 60, 49, 60, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 168, 168, 157, 157, 157, 157, 124, 124, 124, 121, 121, 82, 82, 82, 82, 82, 49, 49, 1, 82, 82] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478401 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478401 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478401/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478401 Building REAL300025478402 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478402' /scratch/stefan/7787258/working/building/REAL300025478402 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478402 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478402/0 /scratch/stefan/7787258/working/building/REAL300025478402 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/280 `/scratch/stefan/7787258/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478402 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 13, 13, 27, 40, 40, 40, 40, 53, 53, 82, 107, 201, 201, 201, 201, 201, 40, 1, 2, 2, 2, 1, 1, 13, 13, 13, 27, 27, 40, 40, 40, 40, 40, 82, 82, 201, 40, 40] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478402 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 125, 201, 201, 77, 75, 77, 70, 75, 45, 45, 45, 45, 38, 31, 38, 12, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 125, 201, 75, 75, 75, 70, 70, 45, 45, 45, 45, 45, 31, 31, 1, 45, 45] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 689 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478402 none CC1=CC=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 17, 40, 40, 10, 9, 10, 6, 9, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 45, 45, 45, 45, 45, 1, 40, 40, 40, 40, 17, 40, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 9, 9, 45, 1, 1] 201 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478402 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478402 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478402/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478402 Building REAL300025478403 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478403' /scratch/stefan/7787258/working/building/REAL300025478403 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478403 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478403/0 /scratch/stefan/7787258/working/building/REAL300025478403 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/281 `/scratch/stefan/7787258/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCCF) `REAL300025478403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478403 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 48, 48, 48, 48, 48, 1, 11, 22, 22, 24, 25, 26, 27, 45, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 48, 1, 1, 24, 24, 25, 25, 26, 26, 27, 27, 45, 45] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478403 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCCCCF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 117, 48, 48, 48, 48, 34, 27, 34, 13, 1, 1, 1, 1, 1, 1, 1, 48, 160, 196, 196, 200, 200, 200, 201, 201, 160, 160, 160, 117, 117, 48, 48, 48, 48, 48, 27, 27, 1, 48, 48, 200, 200, 200, 200, 200, 200, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478403 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478403 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478403/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478403 Building REAL300025478404 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478404' /scratch/stefan/7787258/working/building/REAL300025478404 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478404 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478404/0 /scratch/stefan/7787258/working/building/REAL300025478404 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/282 `/scratch/stefan/7787258/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2(CC2F)C1) `REAL300025478404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478404 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2(CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 51, 51, 51, 51, 51, 1, 13, 26, 26, 37, 37, 37, 37, 37, 37, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 12, 12, 51, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478404 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2(CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 26, 37, 37, 37, 37, 52, 52, 97, 122, 201, 201, 201, 201, 201, 37, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 26, 26, 37, 37, 37, 37, 37, 97, 97, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 575 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: REAL300025478404 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2(CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 104, 51, 51, 51, 51, 39, 33, 39, 12, 1, 1, 1, 1, 1, 1, 1, 51, 124, 165, 165, 201, 201, 201, 201, 201, 201, 124, 124, 124, 104, 104, 51, 51, 51, 51, 51, 33, 33, 1, 51, 51, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 763 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478404 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478404 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478404/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478404 Building REAL300025478405 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478405' /scratch/stefan/7787258/working/building/REAL300025478405 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478405 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478405/0 /scratch/stefan/7787258/working/building/REAL300025478405 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/283 `/scratch/stefan/7787258/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478405 none COC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 11, 24, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 58, 58, 58, 58, 58, 1, 36, 36, 36, 24, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 210 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: REAL300025478405 none COC(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 201, 123, 123, 113, 123, 58, 58, 58, 58, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 123, 123, 123, 113, 113, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58] 201 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 873 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478405 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478405 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478405/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478405 Building REAL300025478406 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478406' /scratch/stefan/7787258/working/building/REAL300025478406 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478406 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478406/0 /scratch/stefan/7787258/working/building/REAL300025478406 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/284 `/scratch/stefan/7787258/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1) `REAL300025478406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478406 none CCC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 5, 5, 5, 5, 12, 21, 21, 21, 21, 32, 32, 51, 71, 133, 133, 133, 133, 133, 21, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 12, 12, 21, 21, 21, 21, 21, 51, 51, 133, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478406 none CCC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 110, 110, 110, 91, 110, 51, 51, 51, 51, 39, 37, 39, 12, 1, 1, 1, 1, 1, 1, 1, 51, 133, 133, 133, 201, 201, 201, 201, 201, 110, 110, 110, 91, 91, 51, 51, 51, 51, 51, 37, 37, 1, 51, 51, 133] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 866 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478406 none CCC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [39, 21, 21, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 51, 51, 51, 51, 51, 1, 21, 21, 21, 39, 39, 39, 39, 39, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 10, 10, 51, 1, 1, 21] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478406 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478406 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478406/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478406 Building REAL300025478407 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478407' /scratch/stefan/7787258/working/building/REAL300025478407 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478407 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478407/0 /scratch/stefan/7787258/working/building/REAL300025478407 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/285 `/scratch/stefan/7787258/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1=NOC=C1) `REAL300025478407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478407 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 8, 12, 1, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 59, 59, 59, 59, 59, 1, 12, 17, 17, 30, 41, 43, 43, 43, 43, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 59, 1, 1, 30, 30, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478407 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 8, 12, 1, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 15, 16, 33, 43, 43, 43, 43, 57, 57, 84, 116, 201, 201, 201, 201, 201, 43, 8, 15, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 43, 43, 43, 43, 43, 84, 84, 201, 43, 43, 8, 8, 1, 1] 201 rigid atoms, others: [44, 45, 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]) total number of confs: 542 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478407 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 1, 8, 12, 1, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 118, 59, 59, 59, 59, 42, 35, 42, 13, 1, 1, 1, 1, 1, 1, 1, 59, 137, 145, 145, 179, 201, 201, 201, 201, 201, 137, 137, 137, 118, 118, 59, 59, 59, 59, 59, 35, 35, 1, 59, 59, 179, 179, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478407 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478407 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478407/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478407 Building REAL300025478408 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478408' /scratch/stefan/7787258/working/building/REAL300025478408 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478408 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478408/0 /scratch/stefan/7787258/working/building/REAL300025478408 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/286 `/scratch/stefan/7787258/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C) `REAL300025478408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478408 none CC1=COC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 19, 38, 38, 38, 38, 53, 53, 87, 115, 201, 201, 201, 201, 201, 38, 1, 1, 2, 2, 2, 1, 9, 9, 9, 19, 19, 38, 38, 38, 38, 38, 87, 87, 201, 38, 38, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478408 none CC1=COC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 151, 151, 151, 121, 151, 58, 58, 58, 58, 44, 36, 44, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 151, 151, 151, 121, 121, 58, 58, 58, 58, 58, 36, 36, 1, 58, 58, 201, 201, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478408 none CC1=COC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 15, 13, 15, 6, 13, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 58, 58, 58, 58, 58, 1, 38, 38, 38, 38, 38, 38, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 10, 10, 58, 1, 1, 38, 38, 38] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478408 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478408 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478408/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478408 Building REAL300025478409 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478409' /scratch/stefan/7787258/working/building/REAL300025478409 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478409 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478409/0 /scratch/stefan/7787258/working/building/REAL300025478409 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/287 `/scratch/stefan/7787258/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CC=N1) `REAL300025478409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478409 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 63, 63, 63, 63, 63, 1, 13, 23, 23, 41, 47, 47, 47, 47, 47, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 63, 1, 1, 41, 41, 47, 47, 47] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 290 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: REAL300025478409 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 21, 35, 47, 47, 47, 47, 57, 57, 109, 127, 201, 201, 201, 201, 201, 47, 5, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 35, 35, 47, 47, 47, 47, 47, 109, 109, 201, 47, 47, 5, 5, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 632 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: REAL300025478409 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 1, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 113, 63, 63, 63, 63, 46, 34, 46, 13, 1, 1, 1, 1, 1, 1, 1, 63, 126, 165, 165, 190, 201, 201, 201, 201, 201, 126, 126, 126, 113, 113, 63, 63, 63, 63, 63, 34, 34, 1, 63, 63, 190, 190, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 776 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478409 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478409 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478409/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478409 Building REAL300025478410 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478410' /scratch/stefan/7787258/working/building/REAL300025478410 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478410 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478410/0 /scratch/stefan/7787258/working/building/REAL300025478410 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/288 `/scratch/stefan/7787258/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1OCCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478410 none CCC1OCCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 17, 32, 32, 32, 32, 45, 45, 89, 116, 201, 201, 201, 201, 201, 32, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 32, 32, 32, 32, 32, 89, 89, 201, 32, 32] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478410 none CCC1OCCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 186, 180, 186, 154, 180, 77, 77, 77, 77, 58, 42, 58, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 154, 154, 77, 77, 77, 77, 77, 42, 42, 1, 77, 77] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 773 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478410 none CCC1OCCC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 32, 32, 32, 32, 32, 21, 15, 21, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 77, 77, 77, 77, 77, 1, 37, 37, 37, 37, 37, 32, 32, 32, 32, 32, 32, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 15, 15, 77, 1, 1] 201 rigid atoms, others: [11, 47, 44, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478410 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478410 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478410/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478410 Building REAL300025478411 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478411' /scratch/stefan/7787258/working/building/REAL300025478411 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478411 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478411/0 /scratch/stefan/7787258/working/building/REAL300025478411 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/289 `/scratch/stefan/7787258/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC1CC2) `REAL300025478411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478411 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 47, 47, 47, 47, 47, 1, 18, 33, 33, 33, 33, 33, 33, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 6, 6, 47, 1, 1, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478411 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 21, 33, 33, 33, 33, 46, 46, 74, 108, 201, 201, 201, 201, 201, 33, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 33, 33, 33, 33, 33, 74, 74, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 545 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478411 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 115, 47, 47, 47, 47, 33, 24, 33, 11, 1, 1, 1, 1, 1, 1, 1, 47, 149, 201, 201, 201, 201, 201, 201, 149, 149, 149, 115, 115, 47, 47, 47, 47, 47, 24, 24, 1, 47, 47, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478411 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478411 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478411/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478411 Building REAL300025478412 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478412' /scratch/stefan/7787258/working/building/REAL300025478412 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478412 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478412/0 /scratch/stefan/7787258/working/building/REAL300025478412 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/290 `/scratch/stefan/7787258/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478412 none CCCC(C)=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 17, 17, 17, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 51, 51, 51, 51, 51, 1, 44, 44, 44, 44, 44, 43, 43, 17, 17, 17, 17, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 9, 9, 51, 1, 1] 201 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478412 none CCCC(C)=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 122, 122, 88, 88, 88, 81, 88, 51, 51, 51, 51, 42, 31, 42, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 88, 88, 88, 81, 81, 51, 51, 51, 51, 51, 31, 31, 1, 51, 51] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 949 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478412 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478412 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478412/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478412 Building REAL300025478413 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478413' /scratch/stefan/7787258/working/building/REAL300025478413 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478413 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478413/0 /scratch/stefan/7787258/working/building/REAL300025478413 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/291 `/scratch/stefan/7787258/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478413 none C=C[C@H](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 23, 27, 27, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 65, 65, 65, 65, 65, 1, 29, 29, 29, 27, 27, 27, 23, 23, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 16, 16, 65, 1, 1] 201 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478413 none C=C[C@H](C)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 201, 137, 137, 137, 124, 137, 65, 65, 65, 65, 44, 35, 44, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 198, 198, 137, 137, 137, 124, 124, 65, 65, 65, 65, 65, 35, 35, 1, 65, 65] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478413 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478413 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478413/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478413 Building REAL300025478414 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478414' /scratch/stefan/7787258/working/building/REAL300025478414 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478414 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478414/0 /scratch/stefan/7787258/working/building/REAL300025478414 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/292 `/scratch/stefan/7787258/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CC1) `REAL300025478414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478414 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 43, 43, 43, 43, 43, 1, 8, 14, 14, 22, 22, 44, 44, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 43, 1, 1, 22, 22, 44, 44, 44, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478414 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 38, 44, 44, 44, 44, 67, 67, 86, 118, 201, 201, 201, 201, 201, 44, 6, 18, 6, 1, 1, 1, 1, 18, 18, 18, 38, 38, 44, 44, 44, 44, 44, 86, 86, 201, 44, 44, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 40, 41]) total number of confs: 555 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: REAL300025478414 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 86, 43, 43, 43, 43, 39, 34, 39, 13, 1, 1, 1, 1, 1, 1, 1, 43, 112, 131, 131, 162, 162, 201, 201, 112, 112, 112, 86, 86, 43, 43, 43, 43, 43, 34, 34, 1, 43, 43, 162, 162, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 791 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478414 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478414 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478414/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478414 Building REAL300025478415 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478415' /scratch/stefan/7787258/working/building/REAL300025478415 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478415 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478415/0 /scratch/stefan/7787258/working/building/REAL300025478415 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/293 `/scratch/stefan/7787258/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CC1)O2) `REAL300025478415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478415 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CC1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 56, 56, 56, 56, 56, 1, 15, 26, 26, 34, 34, 34, 34, 34, 34, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 10, 10, 56, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478415 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CC1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 22, 34, 34, 34, 34, 48, 48, 80, 106, 201, 201, 201, 201, 201, 34, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 34, 34, 34, 34, 34, 80, 80, 201, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 543 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478415 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CCC(CC1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 116, 56, 56, 56, 56, 40, 34, 40, 12, 1, 1, 1, 1, 1, 1, 1, 56, 149, 185, 185, 201, 201, 201, 201, 201, 201, 149, 149, 149, 116, 116, 56, 56, 56, 56, 56, 34, 34, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478415 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478415 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478415/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478415 Building REAL300025478416 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478416' /scratch/stefan/7787258/working/building/REAL300025478416 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478416 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478416/0 /scratch/stefan/7787258/working/building/REAL300025478416 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/294 `/scratch/stefan/7787258/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478416 none CC=C(CC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 17, 27, 34, 13, 17, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 58, 58, 58, 58, 58, 1, 27, 27, 27, 27, 34, 34, 34, 34, 34, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478416 none CC=C(CC)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 127, 198, 201, 126, 127, 113, 126, 58, 58, 58, 58, 46, 36, 46, 13, 1, 1, 1, 1, 1, 1, 1, 58, 198, 198, 198, 198, 201, 201, 201, 201, 201, 126, 126, 126, 113, 113, 58, 58, 58, 58, 58, 36, 36, 1, 58, 58] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478416 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478416 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478416/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478416 Building REAL300025478417 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478417' /scratch/stefan/7787258/working/building/REAL300025478417 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478417 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478417/0 /scratch/stefan/7787258/working/building/REAL300025478417 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/295 `/scratch/stefan/7787258/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1) `REAL300025478417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478417 none CC1=C(F)C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 11, 18, 18, 18, 18, 18, 18, 34, 37, 55, 55, 55, 55, 55, 18, 1, 1, 2, 2, 2, 7, 7, 7, 11, 11, 18, 18, 18, 18, 18, 34, 34, 55, 18, 18, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478417 none CC1=C(F)C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 44, 42, 44, 37, 42, 25, 25, 25, 25, 25, 23, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 55, 55, 55, 55, 55, 42, 42, 42, 37, 37, 25, 25, 25, 25, 25, 23, 23, 1, 25, 25, 55] 55 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478417 none CC1=C(F)C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 12, 10, 12, 5, 10, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 25, 25, 25, 25, 25, 1, 18, 18, 18, 18, 18, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 5, 5, 25, 1, 1, 18] 55 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478417 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478417 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478417/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478417 Building REAL300025478418 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478418' /scratch/stefan/7787258/working/building/REAL300025478418 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478418 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478418/0 /scratch/stefan/7787258/working/building/REAL300025478418 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/296 `/scratch/stefan/7787258/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC12CC(C1)C2) `REAL300025478418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478418 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 62, 62, 62, 62, 62, 1, 10, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 16, 16, 62, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478418 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 12, 19, 19, 19, 19, 41, 41, 76, 112, 201, 201, 201, 201, 201, 19, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 19, 19, 19, 19, 19, 76, 76, 201, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300025478418 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 135, 62, 62, 62, 62, 41, 34, 41, 12, 1, 1, 1, 1, 1, 1, 1, 62, 165, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 135, 135, 62, 62, 62, 62, 62, 34, 34, 1, 62, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478418 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478418 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478418/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478418 Building REAL300025478419 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478419' /scratch/stefan/7787258/working/building/REAL300025478419 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478419 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478419/0 /scratch/stefan/7787258/working/building/REAL300025478419 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/297 `/scratch/stefan/7787258/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(CC#C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478419 none C#CCC(CC#C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 34, 34, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 59, 59, 59, 59, 59, 1, 32, 32, 32, 22, 34, 34, 34, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 59, 1, 1] 201 rigid atoms, others: [48, 43, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 309 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: REAL300025478419 none C#CCC(CC#C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 161, 111, 161, 195, 195, 111, 111, 106, 111, 59, 59, 59, 59, 45, 34, 45, 12, 1, 1, 1, 1, 1, 1, 1, 59, 176, 176, 176, 161, 195, 195, 195, 111, 111, 111, 106, 106, 59, 59, 59, 59, 59, 34, 34, 1, 59, 59] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 987 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478419 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478419 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478419/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478419 Building REAL300025478420 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478420' /scratch/stefan/7787258/working/building/REAL300025478420 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478420 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478420/0 /scratch/stefan/7787258/working/building/REAL300025478420 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/298 `/scratch/stefan/7787258/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)O) `REAL300025478420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478420 none CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 22, 16, 15, 16, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 77, 77, 77, 77, 77, 1, 22, 28, 28, 22, 22, 22, 22, 22, 22, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 16, 16, 77, 1, 1, 28, 28, 28, 28, 84] 603 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 45, 46, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 348 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478420 none CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [153, 153, 150, 149, 150, 138, 149, 77, 77, 77, 77, 54, 40, 54, 13, 1, 1, 1, 1, 1, 1, 1, 77, 153, 201, 201, 153, 153, 153, 153, 153, 153, 149, 149, 149, 138, 138, 77, 77, 77, 77, 77, 40, 40, 1, 77, 77, 201, 201, 201, 201, 603] 603 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1473 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478420 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478420 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478420/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478420 Building REAL300025478421 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478421' /scratch/stefan/7787258/working/building/REAL300025478421 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478421 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478421/0 /scratch/stefan/7787258/working/building/REAL300025478421 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/299 `/scratch/stefan/7787258/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(N)=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478421 none CCC(NC(N)=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 25, 13, 25, 45, 45, 45, 12, 13, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 59, 59, 59, 59, 59, 1, 41, 41, 41, 41, 41, 25, 45, 45, 45, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 59, 1, 1] 201 rigid atoms, others: [45, 43, 41, 42, 11, 12, 13, 14, 15, 16, 49, 50, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 386 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: REAL300025478421 none CCC(NC(N)=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 179, 145, 179, 201, 201, 201, 145, 145, 120, 145, 59, 59, 59, 59, 44, 37, 44, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 179, 201, 201, 201, 145, 145, 145, 120, 120, 59, 59, 59, 59, 59, 37, 37, 1, 59, 59] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 1015 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478421 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478421 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478421/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478421 Building REAL300025478422 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478422' /scratch/stefan/7787258/working/building/REAL300025478422 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478422 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478422/0 /scratch/stefan/7787258/working/building/REAL300025478422 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/300 `/scratch/stefan/7787258/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(CO)=C1) `REAL300025478422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478422 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 78, 78, 78, 78, 78, 1, 13, 21, 21, 26, 26, 26, 26, 42, 26, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 78, 1, 1, 26, 42, 42, 126, 26] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 411 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: REAL300025478422 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 8, 10, 20, 26, 26, 26, 26, 40, 40, 74, 104, 201, 201, 201, 201, 201, 26, 1, 8, 1, 1, 1, 1, 1, 6, 1, 10, 10, 10, 20, 20, 26, 26, 26, 26, 26, 74, 74, 201, 26, 26, 1, 6, 6, 19, 1] 603 rigid atoms, others: [42, 46, 18, 20, 21, 22, 23, 24, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 547 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: REAL300025478422 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(CO)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [177, 149, 78, 78, 78, 78, 62, 44, 62, 13, 1, 1, 1, 1, 1, 1, 1, 78, 177, 197, 197, 201, 201, 201, 201, 201, 201, 177, 177, 177, 149, 149, 78, 78, 78, 78, 78, 44, 44, 1, 78, 78, 201, 201, 201, 603, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1366 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478422 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478422 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478422/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478422 Building REAL300025478423 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478423' /scratch/stefan/7787258/working/building/REAL300025478423 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478423 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478423/0 /scratch/stefan/7787258/working/building/REAL300025478423 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/301 `/scratch/stefan/7787258/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478423 none C=CC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 32, 29, 32, 32, 15, 29, 5, 15, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 70, 70, 70, 70, 70, 1, 43, 43, 43, 32, 32, 32, 96, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 12, 12, 70, 1, 1] 603 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 358 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478423 none C=CC(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 196, 201, 201, 170, 196, 138, 170, 70, 70, 70, 70, 51, 39, 51, 12, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 603, 170, 170, 170, 138, 138, 70, 70, 70, 70, 70, 39, 39, 1, 70, 70] 603 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 1401 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478423 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478423 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478423/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478423 Building REAL300025478424 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478424' /scratch/stefan/7787258/working/building/REAL300025478424 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478424 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478424/0 /scratch/stefan/7787258/working/building/REAL300025478424 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/302 `/scratch/stefan/7787258/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1(O)CCC1) `REAL300025478424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478424 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 49, 49, 49, 49, 49, 1, 12, 22, 22, 23, 23, 38, 38, 38, 38, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 7, 7, 49, 1, 1, 23, 23, 23, 23, 114, 38, 38, 38, 38, 38, 38] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478424 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 13, 27, 38, 38, 38, 38, 48, 48, 76, 111, 201, 201, 201, 201, 201, 38, 5, 8, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 38, 38, 38, 38, 38, 76, 76, 201, 38, 38, 5, 5, 5, 5, 6, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [47, 48, 49, 50, 51, 52, 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]) total number of confs: 565 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478424 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [145, 112, 49, 49, 49, 49, 34, 26, 34, 13, 1, 1, 1, 1, 1, 1, 1, 49, 145, 194, 194, 194, 194, 201, 201, 201, 201, 145, 145, 145, 112, 112, 49, 49, 49, 49, 49, 26, 26, 1, 49, 49, 194, 194, 194, 194, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478424 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478424 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478424/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478424 Building REAL300025478425 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478425' /scratch/stefan/7787258/working/building/REAL300025478425 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478425 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478425/0 /scratch/stefan/7787258/working/building/REAL300025478425 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/303 `/scratch/stefan/7787258/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478425 none CCC(C)(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 19, 12, 16, 6, 12, 1, 1, 1, 1, 1, 1, 4, 4, 12, 21, 81, 81, 81, 81, 81, 1, 20, 20, 20, 20, 20, 16, 16, 16, 19, 19, 57, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 12, 12, 81, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 287 number of broken/clashed sets: 603 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478425 none CCC(C)(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 198, 198, 198, 198, 201, 186, 198, 154, 186, 81, 81, 81, 81, 57, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 198, 198, 198, 201, 201, 603, 186, 186, 186, 154, 154, 81, 81, 81, 81, 81, 28, 28, 1, 81, 81] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1373 number of broken/clashed sets: 603 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478425 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478425 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478425/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478425 Building REAL300025478426 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478426' /scratch/stefan/7787258/working/building/REAL300025478426 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478426 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478426/0 /scratch/stefan/7787258/working/building/REAL300025478426 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/304 `/scratch/stefan/7787258/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1([NH+](C)C)CC1) `REAL300025478426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478426 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1([NH+](C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 11, 11, 11, 11, 11, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 8, 8, 11, 1, 1, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5] 16 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 62 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: REAL300025478426 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1([NH+](C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 4, 5, 5, 5, 5, 8, 8, 13, 13, 16, 16, 16, 16, 16, 5, 1, 3, 1, 1, 4, 4, 4, 1, 1, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 13, 13, 16, 5, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 16 rigid atoms, others: [50, 48, 49, 18, 51, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 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: REAL300025478426 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1([NH+](C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 11, 11, 11, 11, 10, 9, 10, 8, 1, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 11, 11, 11, 11, 11, 9, 9, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478426 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478426/1 /scratch/stefan/7787258/working/building/REAL300025478426 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/305 `/scratch/stefan/7787258/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478426.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478426 none CN(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 5, 5, 9, 9, 17, 28, 28, 28, 28, 41, 41, 74, 107, 201, 201, 201, 201, 201, 28, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 17, 17, 28, 28, 28, 28, 28, 74, 74, 201, 28, 28, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 47, 48, 49, 50, 24, 25] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 531 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478426 none CN(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 194, 145, 194, 123, 145, 56, 56, 56, 56, 43, 35, 43, 12, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 123, 123, 56, 56, 56, 56, 56, 35, 35, 1, 56, 56, 201, 201, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50]) total number of confs: 782 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: REAL300025478426 none CN(C)C1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 23, 12, 23, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 20, 56, 56, 56, 56, 56, 1, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 56, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478426 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478426 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478426/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478426/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478426 Building REAL300025478427 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478427' /scratch/stefan/7787258/working/building/REAL300025478427 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478427 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478427/0 /scratch/stefan/7787258/working/building/REAL300025478427 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/306 `/scratch/stefan/7787258/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC[NH+]1CCCC1) `REAL300025478427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478427 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 10, 16, 62, 62, 62, 62, 62, 1, 14, 23, 23, 29, 33, 37, 37, 37, 37, 37, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 10, 10, 62, 1, 1, 29, 29, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 245 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: REAL300025478427 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 18, 25, 37, 37, 37, 37, 39, 39, 64, 100, 201, 201, 201, 201, 201, 37, 7, 10, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 37, 37, 37, 37, 37, 64, 64, 201, 37, 37, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [54, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 511 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: REAL300025478427 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC[NH+]1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 110, 62, 62, 62, 62, 55, 33, 55, 13, 1, 1, 1, 1, 1, 1, 1, 62, 132, 165, 165, 193, 201, 201, 201, 201, 201, 201, 132, 132, 132, 110, 110, 62, 62, 62, 62, 62, 33, 33, 1, 62, 62, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 839 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478427 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478427 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478427/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478427 Building REAL300025478428 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478428' /scratch/stefan/7787258/working/building/REAL300025478428 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478428 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478428/0 /scratch/stefan/7787258/working/building/REAL300025478428 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/307 `/scratch/stefan/7787258/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1CC1(C)C) `REAL300025478428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478428 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 47, 47, 47, 47, 47, 1, 13, 22, 22, 24, 24, 35, 35, 35, 35, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 47, 1, 1, 24, 24, 24, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478428 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 12, 25, 35, 35, 35, 35, 46, 46, 69, 105, 201, 201, 201, 201, 201, 35, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 35, 35, 35, 35, 35, 69, 69, 201, 35, 35, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [46, 47, 48, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478428 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CCC1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 47, 47, 47, 47, 31, 24, 31, 13, 1, 1, 1, 1, 1, 1, 1, 47, 151, 195, 195, 200, 200, 201, 201, 201, 201, 151, 151, 151, 110, 110, 47, 47, 47, 47, 47, 24, 24, 1, 47, 47, 200, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478428 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478428 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478428/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478428 Building REAL300025478429 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478429' /scratch/stefan/7787258/working/building/REAL300025478429 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478429 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478429/0 /scratch/stefan/7787258/working/building/REAL300025478429 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/308 `/scratch/stefan/7787258/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCCO1) `REAL300025478429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478429 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 18, 61, 61, 61, 61, 61, 1, 11, 20, 20, 33, 33, 36, 36, 36, 36, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 61, 1, 1, 33, 33, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 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: REAL300025478429 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 30, 36, 36, 36, 36, 48, 48, 86, 118, 201, 201, 201, 201, 201, 36, 6, 14, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 36, 36, 36, 36, 36, 86, 86, 201, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 551 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478429 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 61, 61, 61, 61, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 61, 142, 170, 170, 201, 201, 201, 201, 201, 201, 142, 142, 142, 118, 118, 61, 61, 61, 61, 61, 36, 36, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 762 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478429 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478429 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478429/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478429 Building REAL300025478430 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478430' /scratch/stefan/7787258/working/building/REAL300025478430 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478430 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478430/0 /scratch/stefan/7787258/working/building/REAL300025478430 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/309 `/scratch/stefan/7787258/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C)(C1)CO2) `REAL300025478430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478430 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C)(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 56, 56, 56, 56, 56, 1, 16, 27, 27, 32, 32, 32, 32, 32, 32, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 12, 12, 56, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478430 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C)(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 23, 32, 32, 32, 32, 50, 50, 90, 115, 201, 201, 201, 201, 201, 32, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 32, 32, 32, 32, 32, 90, 90, 201, 32, 32, 1, 1, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 50, 47, 48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478430 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C)(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 115, 56, 56, 56, 56, 42, 34, 42, 13, 1, 1, 1, 1, 1, 1, 1, 56, 138, 190, 190, 201, 201, 201, 201, 201, 201, 138, 138, 138, 115, 115, 56, 56, 56, 56, 56, 34, 34, 1, 56, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 751 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478430 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478430 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478430/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478430 Building REAL300025478431 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478431' /scratch/stefan/7787258/working/building/REAL300025478431 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478431 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478431/0 /scratch/stefan/7787258/working/building/REAL300025478431 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/310 `/scratch/stefan/7787258/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(O)CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478431 none C#CC1(O)CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 28, 43, 43, 43, 43, 63, 63, 104, 133, 201, 201, 201, 201, 201, 43, 1, 1, 6, 1, 1, 1, 11, 11, 11, 28, 28, 43, 43, 43, 43, 43, 104, 104, 201, 43, 43, 1, 1] 603 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 48, 26, 27, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 582 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: REAL300025478431 none C#CC1(O)CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 139, 133, 139, 120, 133, 61, 61, 61, 61, 47, 35, 47, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 603, 201, 201, 201, 133, 133, 133, 120, 120, 61, 61, 61, 61, 61, 35, 35, 1, 61, 61, 201, 201] 603 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 1392 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: REAL300025478431 none C#CC1(O)CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 17, 12, 17, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 61, 61, 61, 61, 61, 1, 43, 43, 129, 43, 43, 43, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 14, 14, 61, 1, 1, 43, 43] 603 rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48]) total number of confs: 369 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478431 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478431 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478431/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478431 Building REAL300025478432 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478432' /scratch/stefan/7787258/working/building/REAL300025478432 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478432 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478432/0 /scratch/stefan/7787258/working/building/REAL300025478432 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/311 `/scratch/stefan/7787258/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478432 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 31, 48, 48, 48, 48, 65, 65, 114, 129, 201, 201, 201, 201, 201, 48, 1, 2, 2, 2, 2, 2, 2, 1, 15, 15, 15, 31, 31, 48, 48, 48, 48, 48, 114, 114, 201, 48, 48, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 621 number of broken/clashed sets: 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: REAL300025478432 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 132, 121, 132, 103, 121, 60, 60, 60, 60, 51, 40, 51, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 103, 103, 60, 60, 60, 60, 60, 40, 40, 1, 60, 60, 201] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 647 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: REAL300025478432 none CC1=C(C)NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 20, 12, 20, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 12, 17, 60, 60, 60, 60, 60, 1, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 60, 1, 1, 48] 201 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49]) total number of confs: 203 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478432 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478432 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478432/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478432 Building REAL300025478433 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478433' /scratch/stefan/7787258/working/building/REAL300025478433 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478433 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478433/0 /scratch/stefan/7787258/working/building/REAL300025478433 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/312 `/scratch/stefan/7787258/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CCCC21) `REAL300025478433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478433 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CCCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 69, 69, 69, 69, 69, 1, 14, 26, 26, 29, 29, 29, 29, 29, 29, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 69, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478433 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CCCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 18, 29, 29, 29, 29, 40, 40, 80, 110, 201, 201, 201, 201, 201, 29, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 29, 29, 29, 29, 29, 80, 80, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478433 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC2CCCC21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 149, 69, 69, 69, 69, 47, 36, 47, 13, 1, 1, 1, 1, 1, 1, 1, 69, 176, 200, 200, 201, 201, 201, 201, 201, 201, 176, 176, 176, 149, 149, 69, 69, 69, 69, 69, 36, 36, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 770 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478433 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478433 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478433/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478433 Building REAL300025478434 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478434' /scratch/stefan/7787258/working/building/REAL300025478434 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478434 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478434/0 /scratch/stefan/7787258/working/building/REAL300025478434 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/313 `/scratch/stefan/7787258/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CO2) `REAL300025478434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478434 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 72, 72, 72, 72, 72, 1, 16, 32, 32, 37, 37, 37, 37, 37, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 12, 12, 72, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478434 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 24, 37, 37, 37, 37, 48, 48, 79, 109, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 37, 37, 37, 37, 37, 79, 79, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 535 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478434 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 141, 72, 72, 72, 72, 52, 44, 52, 13, 1, 1, 1, 1, 1, 1, 1, 72, 176, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 141, 141, 72, 72, 72, 72, 72, 44, 44, 1, 72, 72, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478434 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478434 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478434/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478434 Building REAL300025478435 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478435' /scratch/stefan/7787258/working/building/REAL300025478435 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478435 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478435/0 /scratch/stefan/7787258/working/building/REAL300025478435 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/314 `/scratch/stefan/7787258/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CCC(O)C1) `REAL300025478435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478435 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 51, 51, 51, 51, 51, 1, 15, 25, 25, 27, 43, 43, 43, 43, 43, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 12, 12, 51, 1, 1, 27, 27, 43, 43, 43, 43, 43, 43, 129, 43, 43] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478435 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 9, 17, 29, 43, 43, 43, 43, 58, 58, 106, 129, 201, 201, 201, 201, 201, 43, 5, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 29, 29, 43, 43, 43, 43, 43, 106, 106, 201, 43, 43, 5, 5, 1, 1, 1, 1, 1, 1, 6, 1, 1] 603 rigid atoms, others: [44, 45, 46, 47, 48, 49, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50]) total number of confs: 608 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478435 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [137, 111, 51, 51, 51, 51, 39, 31, 39, 12, 1, 1, 1, 1, 1, 1, 1, 51, 137, 164, 164, 166, 201, 201, 201, 201, 201, 137, 137, 137, 111, 111, 51, 51, 51, 51, 51, 31, 31, 1, 51, 51, 166, 166, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478435 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478435 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478435/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478435 Building REAL300025478436 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478436' /scratch/stefan/7787258/working/building/REAL300025478436 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478436 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478436/0 /scratch/stefan/7787258/working/building/REAL300025478436 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/315 `/scratch/stefan/7787258/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)O) `REAL300025478436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478436 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 24, 15, 18, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 17, 27, 82, 82, 82, 82, 82, 1, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 17, 17, 82, 1, 1, 24, 24, 24, 24, 24, 24, 72] 603 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 314 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478436 none C[C@@H](C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 201, 201, 195, 201, 174, 195, 82, 82, 82, 82, 53, 40, 53, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 174, 174, 82, 82, 82, 82, 82, 40, 40, 1, 82, 82, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1371 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478436 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478436 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478436/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478436 Building REAL300025478437 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478437' /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478437 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478437/0 /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/316 `/scratch/stefan/7787258/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@@H+]2C) `REAL300025478437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 11, 16, 16, 16, 16, 16, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 10, 10, 16, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 17 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 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: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 7, 8, 8, 8, 8, 11, 11, 15, 15, 17, 17, 17, 17, 17, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 15, 15, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52]) total number of confs: 71 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: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 16, 16, 15, 16, 12, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 15, 15, 1, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 36 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478437/1 /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/317 `/scratch/stefan/7787258/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@H+]2C) `REAL300025478437.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 4, 4, 7, 9, 20, 20, 20, 20, 20, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 7, 7, 20, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 23 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 9, 12, 12, 12, 12, 14, 14, 19, 19, 23, 23, 23, 23, 23, 12, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 12, 12, 12, 12, 12, 19, 19, 23, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)C[N@H+]2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 20, 20, 20, 20, 20, 18, 20, 12, 1, 1, 1, 1, 1, 1, 1, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 20, 20, 20, 20, 20, 18, 18, 1, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 65 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478437/2 /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/318 `/scratch/stefan/7787258/working/3D/318' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CN2C) `REAL300025478437.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478437/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CN2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 67, 67, 67, 67, 67, 1, 12, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CN2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 12, 18, 18, 18, 18, 30, 30, 59, 94, 201, 201, 201, 201, 201, 18, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 18, 18, 18, 18, 18, 59, 59, 201, 18, 18, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50, 51]) total number of confs: 494 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478437 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)CN2C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 138, 67, 67, 67, 67, 46, 38, 46, 12, 1, 1, 1, 1, 1, 1, 1, 67, 164, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 138, 138, 67, 67, 67, 67, 67, 38, 38, 1, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478437 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478437 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478437/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478437/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478437/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478437 Building REAL300025478438 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478438' /scratch/stefan/7787258/working/building/REAL300025478438 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478438 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478438/0 /scratch/stefan/7787258/working/building/REAL300025478438 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/319 `/scratch/stefan/7787258/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NN1C) `REAL300025478438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478438 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 51, 51, 51, 51, 51, 1, 12, 25, 25, 38, 46, 46, 46, 46, 46, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 51, 1, 1, 38, 38, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 258 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: REAL300025478438 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 21, 36, 46, 46, 46, 46, 60, 60, 109, 135, 201, 201, 201, 201, 201, 46, 4, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 36, 36, 46, 46, 46, 46, 46, 109, 109, 201, 46, 46, 4, 4, 1, 2, 2, 2] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 605 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: REAL300025478438 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 99, 51, 51, 51, 51, 45, 39, 45, 13, 1, 1, 1, 1, 1, 1, 1, 51, 119, 163, 163, 175, 201, 201, 201, 201, 201, 119, 119, 119, 99, 99, 51, 51, 51, 51, 51, 39, 39, 1, 51, 51, 175, 175, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 744 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478438 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478438 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478438/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478438 Building REAL300025478439 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478439' /scratch/stefan/7787258/working/building/REAL300025478439 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478439 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478439/0 /scratch/stefan/7787258/working/building/REAL300025478439 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/320 `/scratch/stefan/7787258/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)OC2) `REAL300025478439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478439 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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: [16, 6, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 45, 45, 45, 45, 45, 1, 16, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 7, 7, 45, 1, 1, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478439 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 17, 30, 30, 30, 30, 40, 40, 71, 109, 201, 201, 201, 201, 201, 30, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 30, 30, 30, 30, 30, 71, 71, 201, 30, 30, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 537 number of broken/clashed sets: 143 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478439 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 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: [131, 105, 45, 45, 45, 45, 34, 25, 34, 11, 1, 1, 1, 1, 1, 1, 1, 45, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 105, 105, 45, 45, 45, 45, 45, 25, 25, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 748 number of broken/clashed sets: 143 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478439 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478439 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478439/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478439 Building REAL300025478440 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478440' /scratch/stefan/7787258/working/building/REAL300025478440 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478440 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478440/0 /scratch/stefan/7787258/working/building/REAL300025478440 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/321 `/scratch/stefan/7787258/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478440 none CC(O)C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 6, 6, 8, 8, 18, 28, 28, 28, 28, 41, 41, 72, 97, 192, 192, 192, 192, 192, 28, 4, 4, 4, 4, 12, 1, 1, 1, 1, 8, 8, 8, 18, 18, 28, 28, 28, 28, 28, 72, 72, 192, 28, 28] 603 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 529 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: REAL300025478440 none CC(O)C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 192, 201, 192, 192, 146, 136, 146, 120, 136, 55, 55, 55, 55, 41, 34, 41, 12, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 603, 192, 192, 192, 192, 136, 136, 136, 120, 120, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55] 603 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 1393 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: REAL300025478440 none CC(O)C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 28, 38, 28, 28, 14, 11, 14, 6, 11, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 55, 55, 55, 55, 55, 1, 38, 38, 38, 38, 114, 28, 28, 28, 28, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 9, 9, 55, 1, 1] 603 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 356 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478440 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478440 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478440/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478440 Building REAL300025478441 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478441' /scratch/stefan/7787258/working/building/REAL300025478441 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478441 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478441/0 /scratch/stefan/7787258/working/building/REAL300025478441 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/322 `/scratch/stefan/7787258/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12) `REAL300025478441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478441 none C[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 15, 33, 33, 33, 33, 42, 42, 69, 104, 201, 201, 201, 201, 201, 33, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 69, 69, 201, 33, 33, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478441 none C[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 201, 137, 168, 61, 61, 61, 61, 40, 28, 40, 12, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 137, 137, 61, 61, 61, 61, 61, 28, 28, 1, 61, 61, 201, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 772 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478441 none C[C@@H]1C[C@@]2(C(=O)N(C)CC3CCN(C(=O)CSC4=NNC(=O)[N-]4)C3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 17, 33, 6, 17, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 61, 61, 61, 61, 61, 1, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 7, 7, 61, 1, 1, 33, 33] 201 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 47, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478441 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478441 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478441/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478441 Building REAL300025478442 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478442' /scratch/stefan/7787258/working/building/REAL300025478442 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478442 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478442/0 /scratch/stefan/7787258/working/building/REAL300025478442 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/323 `/scratch/stefan/7787258/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1COC(C)(C)C1) `REAL300025478442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478442 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1COC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 6, 7, 14, 24, 65, 65, 65, 65, 65, 1, 15, 28, 28, 37, 37, 37, 37, 37, 37, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 14, 14, 65, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 237 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478442 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1COC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 27, 37, 37, 37, 37, 48, 48, 90, 118, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 37, 37, 37, 37, 37, 90, 90, 201, 37, 37, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [42, 43, 44, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50]) total number of confs: 581 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478442 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1COC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 126, 64, 64, 64, 64, 44, 34, 44, 12, 1, 1, 1, 1, 1, 1, 1, 64, 139, 180, 180, 201, 201, 201, 201, 201, 201, 139, 139, 139, 126, 126, 64, 64, 64, 64, 64, 34, 34, 1, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 746 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478442 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478442 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478442/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478442 Building REAL300025478443 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478443' /scratch/stefan/7787258/working/building/REAL300025478443 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478443 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478443/0 /scratch/stefan/7787258/working/building/REAL300025478443 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/324 `/scratch/stefan/7787258/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NC=N1) `REAL300025478443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478443 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 68, 68, 68, 68, 68, 1, 12, 22, 22, 31, 38, 38, 38, 38, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 68, 1, 1, 31, 31, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 261 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: REAL300025478443 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 33, 38, 38, 38, 38, 58, 58, 95, 124, 201, 201, 201, 201, 201, 38, 5, 15, 1, 1, 1, 1, 1, 1, 23, 23, 23, 33, 33, 38, 38, 38, 38, 38, 95, 95, 201, 38, 38, 5, 5, 1, 1] 201 rigid atoms, others: [43, 44, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 571 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: REAL300025478443 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 128, 68, 68, 68, 68, 48, 43, 48, 13, 1, 1, 1, 1, 1, 1, 1, 68, 153, 180, 180, 195, 201, 201, 201, 201, 153, 153, 153, 128, 128, 68, 68, 68, 68, 68, 43, 43, 1, 68, 68, 195, 195, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 804 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478443 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478443 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478443/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478443 Building REAL300025478444 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478444' /scratch/stefan/7787258/working/building/REAL300025478444 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478444 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478444/0 /scratch/stefan/7787258/working/building/REAL300025478444 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/325 `/scratch/stefan/7787258/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478444 none CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 50, 25, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 68, 68, 68, 68, 68, 1, 50, 50, 50, 50, 50, 50, 25, 25, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 68, 1, 1] 201 rigid atoms, others: [48, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 49, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 265 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: REAL300025478444 none CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 201, 173, 152, 152, 152, 122, 152, 68, 68, 68, 68, 52, 41, 52, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 173, 173, 152, 152, 152, 122, 122, 68, 68, 68, 68, 68, 41, 41, 1, 68, 68] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 781 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478444 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478444 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478444/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478444 Building REAL300025478445 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478445' /scratch/stefan/7787258/working/building/REAL300025478445 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478445 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478445/0 /scratch/stefan/7787258/working/building/REAL300025478445 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/326 `/scratch/stefan/7787258/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(=O)O1) `REAL300025478445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478445 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 69, 69, 69, 69, 69, 1, 15, 33, 33, 51, 51, 51, 51, 51, 51, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 12, 12, 69, 1, 1, 51, 51, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478445 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 32, 51, 51, 51, 51, 63, 63, 99, 121, 201, 201, 201, 201, 201, 51, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 32, 32, 51, 51, 51, 51, 51, 99, 99, 201, 51, 51, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478445 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC(=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 125, 69, 69, 69, 69, 56, 44, 56, 13, 1, 1, 1, 1, 1, 1, 1, 69, 152, 194, 194, 201, 201, 201, 201, 201, 201, 152, 152, 152, 125, 125, 69, 69, 69, 69, 69, 44, 44, 1, 69, 69, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478445 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478445 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478445/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478445 Building REAL300025478446 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478446' /scratch/stefan/7787258/working/building/REAL300025478446 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478446 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478446/0 /scratch/stefan/7787258/working/building/REAL300025478446 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/327 `/scratch/stefan/7787258/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)CC1) `REAL300025478446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478446 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 45, 45, 45, 45, 45, 1, 13, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 8, 8, 45, 1, 1, 26, 26, 26, 26, 26, 26, 26] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478446 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 15, 26, 26, 26, 26, 35, 35, 65, 102, 201, 201, 201, 201, 201, 26, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 26, 26, 26, 26, 26, 65, 65, 201, 26, 26, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 537 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478446 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C#CC1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 117, 45, 45, 45, 45, 31, 23, 31, 13, 1, 1, 1, 1, 1, 1, 1, 45, 145, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 117, 117, 45, 45, 45, 45, 45, 23, 23, 1, 45, 45, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478446 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478446 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478446/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478446 Building REAL300025478447 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478447' /scratch/stefan/7787258/working/building/REAL300025478447 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478447 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478447/0 /scratch/stefan/7787258/working/building/REAL300025478447 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/328 `/scratch/stefan/7787258/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478447 none C=CC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 5, 11, 11, 11, 11, 27, 39, 39, 39, 39, 50, 50, 86, 109, 201, 201, 201, 201, 201, 39, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 11, 27, 27, 39, 39, 39, 39, 39, 86, 86, 201, 39, 39, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478447 none C=CC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 110, 110, 110, 100, 110, 60, 60, 60, 60, 52, 41, 52, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 164, 164, 110, 110, 110, 100, 100, 60, 60, 60, 60, 60, 41, 41, 1, 60, 60, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 857 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478447 none C=CC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 27, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 60, 60, 60, 60, 60, 1, 39, 39, 39, 39, 39, 39, 27, 27, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 11, 11, 60, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478447 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478447 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478447/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478447 Building REAL300025478448 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478448' /scratch/stefan/7787258/working/building/REAL300025478448 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478448 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478448/0 /scratch/stefan/7787258/working/building/REAL300025478448 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/329 `/scratch/stefan/7787258/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1) `REAL300025478448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478448 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 13, 17, 5, 13, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 76, 76, 76, 76, 76, 1, 25, 49, 49, 49, 49, 25, 25, 25, 25, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 76, 1, 1, 49, 49, 49] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 44, 45, 40, 21, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48]) total number of confs: 271 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: REAL300025478448 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 10, 16, 16, 33, 49, 49, 49, 49, 68, 68, 107, 132, 201, 201, 201, 201, 201, 49, 1, 1, 1, 1, 1, 6, 6, 6, 5, 16, 16, 16, 33, 33, 49, 49, 49, 49, 49, 107, 107, 201, 49, 49, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 613 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: REAL300025478448 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 153, 136, 153, 124, 136, 76, 76, 76, 76, 62, 48, 62, 13, 1, 1, 1, 1, 1, 1, 1, 76, 166, 201, 201, 201, 201, 166, 166, 166, 166, 136, 136, 136, 124, 124, 76, 76, 76, 76, 76, 48, 48, 1, 76, 76, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 743 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478448 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478448 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478448/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478448 Building REAL300025478449 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478449' /scratch/stefan/7787258/working/building/REAL300025478449 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478449 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478449/0 /scratch/stefan/7787258/working/building/REAL300025478449 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/330 `/scratch/stefan/7787258/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CNC1=O) `REAL300025478449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478449 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 54, 54, 54, 54, 54, 1, 13, 26, 26, 35, 35, 35, 35, 35, 35, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 12, 12, 54, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478449 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 27, 35, 35, 35, 35, 51, 51, 95, 116, 201, 201, 201, 201, 201, 35, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 27, 27, 35, 35, 35, 35, 35, 95, 95, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 564 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478449 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 120, 54, 54, 54, 54, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 54, 139, 173, 173, 201, 201, 201, 201, 201, 201, 139, 139, 139, 120, 120, 54, 54, 54, 54, 54, 37, 37, 1, 54, 54, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478449 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478449 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478449/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478449 Building REAL300025478450 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478450' /scratch/stefan/7787258/working/building/REAL300025478450 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478450 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478450/0 /scratch/stefan/7787258/working/building/REAL300025478450 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/331 `/scratch/stefan/7787258/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CSC(F)F) `REAL300025478450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478450 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CSC(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 14, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 19, 46, 46, 46, 46, 46, 1, 10, 15, 15, 17, 25, 25, 25, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 46, 1, 1, 17, 17, 25] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478450 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CSC(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 14, 5, 15, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 97, 46, 46, 46, 46, 35, 31, 35, 12, 1, 1, 1, 1, 1, 1, 1, 46, 119, 136, 136, 138, 201, 201, 201, 119, 119, 119, 97, 97, 46, 46, 46, 46, 46, 31, 31, 1, 46, 46, 138, 138, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 666 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478450 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478450 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478450/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478450 Building REAL300025478451 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478451' /scratch/stefan/7787258/working/building/REAL300025478451 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478451 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478451/0 /scratch/stefan/7787258/working/building/REAL300025478451 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/332 `/scratch/stefan/7787258/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478451 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 16, 27, 27, 27, 27, 43, 43, 86, 108, 201, 201, 201, 201, 201, 27, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 27, 27, 27, 27, 27, 86, 86, 201, 27, 27, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 51, 32, 34, 35, 52, 53, 54, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 558 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: REAL300025478451 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 147, 194, 126, 147, 65, 65, 65, 65, 47, 39, 47, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 126, 126, 65, 65, 65, 65, 65, 39, 39, 1, 65, 65, 201, 201, 201, 201] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 782 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: REAL300025478451 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 21, 10, 21, 6, 10, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 65, 65, 65, 65, 65, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 12, 12, 65, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 49, 50, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478451 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478451 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478451/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478451 Building REAL300025478452 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478452' /scratch/stefan/7787258/working/building/REAL300025478452 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478452 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478452/0 /scratch/stefan/7787258/working/building/REAL300025478452 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/333 `/scratch/stefan/7787258/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC=[N+]1[O-]) `REAL300025478452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478452 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC=[N+]1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 61, 61, 61, 61, 61, 1, 14, 29, 29, 34, 34, 34, 34, 34, 34, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 13, 13, 61, 1, 1, 34, 34, 34, 34] 182 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478452 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC=[N+]1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 21, 34, 34, 34, 34, 51, 51, 89, 117, 182, 182, 182, 182, 182, 34, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 34, 34, 34, 34, 34, 89, 89, 182, 34, 34, 1, 1, 1, 1] 182 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 507 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: REAL300025478452 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=CC=[N+]1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [136, 128, 61, 61, 61, 61, 44, 37, 44, 13, 1, 1, 1, 1, 1, 1, 1, 61, 136, 175, 175, 182, 182, 182, 182, 182, 182, 136, 136, 136, 128, 128, 61, 61, 61, 61, 61, 37, 37, 1, 61, 61, 182, 182, 182, 182] 182 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 665 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478452 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478452 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478452/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478452 Building REAL300025478453 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478453' /scratch/stefan/7787258/working/building/REAL300025478453 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478453 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478453/0 /scratch/stefan/7787258/working/building/REAL300025478453 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/334 `/scratch/stefan/7787258/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCC1) `REAL300025478453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478453 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 68, 68, 68, 68, 68, 1, 14, 29, 29, 37, 37, 37, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 13, 13, 68, 1, 1, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478453 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 28, 37, 37, 37, 37, 53, 53, 89, 118, 201, 201, 201, 201, 201, 37, 1, 10, 1, 1, 1, 1, 14, 14, 14, 28, 28, 37, 37, 37, 37, 37, 89, 89, 201, 37, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 556 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: REAL300025478453 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 152, 68, 68, 68, 68, 49, 42, 49, 13, 1, 1, 1, 1, 1, 1, 1, 68, 177, 201, 201, 201, 201, 201, 177, 177, 177, 152, 152, 68, 68, 68, 68, 68, 42, 42, 1, 68, 68, 201, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 763 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478453 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478453 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478453/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478453 Building REAL300025478454 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478454' /scratch/stefan/7787258/working/building/REAL300025478454 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478454 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478454/0 /scratch/stefan/7787258/working/building/REAL300025478454 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/335 `/scratch/stefan/7787258/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(F)O1) `REAL300025478454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478454 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 15, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 56, 56, 56, 56, 56, 1, 11, 28, 28, 32, 32, 32, 32, 32, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 56, 1, 1, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478454 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 15, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 25, 32, 32, 32, 32, 48, 48, 82, 111, 201, 201, 201, 201, 201, 32, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 32, 32, 32, 32, 32, 82, 82, 201, 32, 32, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478454 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 15, 12, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 116, 56, 56, 56, 56, 40, 36, 40, 13, 1, 1, 1, 1, 1, 1, 1, 56, 135, 199, 199, 201, 201, 201, 201, 201, 135, 135, 135, 116, 116, 56, 56, 56, 56, 56, 36, 36, 1, 56, 56, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478454 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478454 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478454/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478454 Building REAL300025478455 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478455' /scratch/stefan/7787258/working/building/REAL300025478455 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478455 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478455/0 /scratch/stefan/7787258/working/building/REAL300025478455 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/336 `/scratch/stefan/7787258/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478455 none CON=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 28, 28, 14, 11, 14, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 66, 66, 66, 66, 66, 1, 32, 32, 32, 28, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 66, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478455 none CON=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 148, 158, 134, 148, 66, 66, 66, 66, 48, 37, 48, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 148, 148, 148, 134, 134, 66, 66, 66, 66, 66, 37, 37, 1, 66, 66] 201 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 777 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478455 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478455 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478455/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478455 Building REAL300025478456 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478456' /scratch/stefan/7787258/working/building/REAL300025478456 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478456 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478456/0 /scratch/stefan/7787258/working/building/REAL300025478456 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/337 `/scratch/stefan/7787258/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478456 none C#CCC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 14, 21, 6, 14, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 47, 47, 47, 47, 47, 1, 24, 24, 24, 21, 21, 21, 21, 21, 21, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 7, 7, 47, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478456 none C#CCC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 199, 199, 199, 141, 199, 116, 141, 47, 47, 47, 47, 33, 25, 33, 12, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 199, 199, 199, 199, 199, 199, 141, 141, 141, 116, 116, 47, 47, 47, 47, 47, 25, 25, 1, 47, 47] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 784 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478456 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478456 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478456/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478456 Building REAL300025478457 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478457' /scratch/stefan/7787258/working/building/REAL300025478457 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478457 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478457/0 /scratch/stefan/7787258/working/building/REAL300025478457 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/338 `/scratch/stefan/7787258/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(N)=O) `REAL300025478457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478457 none CN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 38, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 62, 62, 62, 62, 62, 1, 44, 52, 52, 44, 44, 44, 38, 38, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 62, 1, 1, 52, 52] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 45, 44, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47]) total number of confs: 299 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478457 none CN(CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 185, 122, 122, 122, 106, 122, 62, 62, 62, 62, 52, 43, 52, 13, 1, 1, 1, 1, 1, 1, 1, 62, 195, 201, 201, 195, 195, 195, 185, 185, 122, 122, 122, 106, 106, 62, 62, 62, 62, 62, 43, 43, 1, 62, 62, 201, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 831 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478457 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478457 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478457/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478457 Building REAL300025478458 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478458' /scratch/stefan/7787258/working/building/REAL300025478458 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478458 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478458/0 /scratch/stefan/7787258/working/building/REAL300025478458 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/339 `/scratch/stefan/7787258/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC(=O)N[N-]1) `REAL300025478458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478458 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 80, 80, 80, 80, 80, 1, 12, 20, 20, 37, 37, 37, 37, 37, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 11, 11, 80, 1, 1, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478458 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 26, 37, 37, 37, 37, 45, 45, 84, 116, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 37, 37, 37, 37, 37, 84, 84, 201, 37, 37, 1] 201 rigid atoms, others: [41, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478458 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 129, 80, 80, 80, 80, 55, 47, 55, 13, 1, 1, 1, 1, 1, 1, 1, 80, 147, 155, 155, 201, 201, 201, 201, 201, 147, 147, 147, 129, 129, 80, 80, 80, 80, 80, 47, 47, 1, 80, 80, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478458 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478458 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478458/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478458 Building REAL300025478459 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478459' /scratch/stefan/7787258/working/building/REAL300025478459 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478459 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478459/0 /scratch/stefan/7787258/working/building/REAL300025478459 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/340 `/scratch/stefan/7787258/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CC1) `REAL300025478459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478459 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 39, 39, 39, 39, 39, 1, 10, 18, 18, 30, 30, 30, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 5, 5, 39, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 17, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478459 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 20, 30, 30, 30, 30, 37, 37, 58, 89, 201, 201, 201, 201, 201, 30, 1, 4, 1, 1, 1, 1, 9, 9, 9, 20, 20, 30, 30, 30, 30, 30, 58, 58, 201, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478459 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 76, 39, 39, 39, 39, 27, 25, 27, 11, 1, 1, 1, 1, 1, 1, 1, 39, 106, 142, 142, 201, 201, 201, 106, 106, 106, 76, 76, 39, 39, 39, 39, 39, 25, 25, 1, 39, 39, 201, 201, 201, 201] 201 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478459 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478459 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478459/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478459 Building REAL300025478460 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478460' /scratch/stefan/7787258/working/building/REAL300025478460 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478460 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478460/0 /scratch/stefan/7787258/working/building/REAL300025478460 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/341 `/scratch/stefan/7787258/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)C1CC1) `REAL300025478460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478460 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 42, 42, 42, 42, 42, 1, 9, 19, 19, 19, 19, 19, 31, 31, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 11, 11, 42, 1, 1, 31, 31, 31, 31, 31] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478460 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 22, 31, 31, 31, 31, 51, 51, 83, 111, 201, 201, 201, 201, 201, 31, 4, 7, 1, 4, 4, 1, 1, 1, 11, 11, 11, 22, 22, 31, 31, 31, 31, 31, 83, 83, 201, 31, 31, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 530 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478460 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)(F)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 15, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 91, 42, 42, 42, 42, 30, 27, 30, 10, 1, 1, 1, 1, 1, 1, 1, 42, 106, 126, 126, 126, 126, 126, 201, 201, 106, 106, 106, 91, 91, 42, 42, 42, 42, 42, 27, 27, 1, 42, 42, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478460 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478460 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478460/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478460 Building REAL300025478461 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478461' /scratch/stefan/7787258/working/building/REAL300025478461 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478461 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478461/0 /scratch/stefan/7787258/working/building/REAL300025478461 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/342 `/scratch/stefan/7787258/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COCCO) `REAL300025478461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478461 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COCCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 55, 55, 55, 55, 55, 1, 10, 11, 11, 18, 25, 37, 40, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 55, 1, 1, 18, 18, 37, 37, 40, 40, 120] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 386 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478461 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COCCO NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 108, 55, 55, 55, 55, 45, 34, 45, 12, 1, 1, 1, 1, 1, 1, 1, 55, 121, 122, 122, 179, 198, 201, 201, 121, 121, 121, 108, 108, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55, 179, 179, 201, 201, 201, 201, 603] 603 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1472 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478461 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478461 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478461/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478461 Building REAL300025478462 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478462' /scratch/stefan/7787258/working/building/REAL300025478462 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478462 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478462/0 /scratch/stefan/7787258/working/building/REAL300025478462 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/343 `/scratch/stefan/7787258/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(C)(C)C1) `REAL300025478462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478462 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 18, 59, 59, 59, 59, 59, 1, 12, 21, 21, 40, 40, 40, 40, 40, 40, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 59, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478462 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 30, 40, 40, 40, 40, 63, 63, 107, 131, 201, 201, 201, 201, 201, 40, 1, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 40, 40, 40, 40, 40, 107, 107, 201, 40, 40, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [48, 49, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 616 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478462 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 130, 59, 59, 59, 59, 48, 40, 48, 13, 1, 1, 1, 1, 1, 1, 1, 59, 156, 184, 184, 201, 201, 201, 201, 201, 201, 156, 156, 156, 130, 130, 59, 59, 59, 59, 59, 40, 40, 1, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478462 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478462 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478462/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478462 Building REAL300025478463 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478463' /scratch/stefan/7787258/working/building/REAL300025478463 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478463 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478463/0 /scratch/stefan/7787258/working/building/REAL300025478463 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/344 `/scratch/stefan/7787258/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=C(F)C=N1) `REAL300025478463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478463 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 15, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 59, 59, 59, 59, 59, 1, 13, 24, 24, 28, 28, 28, 28, 28, 28, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 9, 9, 59, 1, 1, 28, 28] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478463 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 15, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 24, 32, 32, 32, 32, 46, 46, 80, 109, 201, 201, 201, 201, 201, 32, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 24, 24, 32, 32, 32, 32, 32, 80, 80, 201, 32, 32, 1, 1] 201 rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 528 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478463 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=C(F)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 15, 1, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 116, 59, 59, 59, 59, 45, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 59, 163, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 116, 116, 59, 59, 59, 59, 59, 27, 27, 1, 59, 59, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478463 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478463 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478463/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478463 Building REAL300025478464 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478464' /scratch/stefan/7787258/working/building/REAL300025478464 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478464 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478464/0 /scratch/stefan/7787258/working/building/REAL300025478464 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/345 `/scratch/stefan/7787258/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CF) `REAL300025478464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478464 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 12, 12, 12, 21, 21, 21, 27, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1, 21, 21, 21, 21, 21, 21, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478464 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(C)(C)CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 82, 46, 46, 46, 46, 31, 27, 31, 12, 1, 1, 1, 1, 1, 1, 1, 46, 109, 109, 109, 201, 201, 201, 201, 109, 109, 109, 82, 82, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 936 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478464 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478464 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478464/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478464 Building REAL300025478465 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478465' /scratch/stefan/7787258/working/building/REAL300025478465 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478465 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478465/0 /scratch/stefan/7787258/working/building/REAL300025478465 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/346 `/scratch/stefan/7787258/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478465 none CC(C)[C@@H](O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 31, 37, 23, 31, 31, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 87, 87, 87, 87, 87, 1, 37, 37, 37, 37, 37, 37, 37, 93, 23, 23, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 16, 16, 87, 1, 1] 603 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478465 none CC(C)[C@@H](O)CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 194, 201, 192, 194, 194, 171, 171, 171, 158, 171, 87, 87, 87, 87, 62, 47, 62, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 582, 192, 192, 171, 171, 171, 158, 158, 87, 87, 87, 87, 87, 47, 47, 1, 87, 87] 603 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1396 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478465 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478465 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478465/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478465 Building REAL300025478466 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478466' /scratch/stefan/7787258/working/building/REAL300025478466 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478466 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478466/0 /scratch/stefan/7787258/working/building/REAL300025478466 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/347 `/scratch/stefan/7787258/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478466 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 5, 5, 9, 9, 23, 31, 31, 31, 31, 46, 46, 81, 107, 201, 201, 201, 201, 201, 31, 1, 1, 5, 5, 5, 9, 9, 9, 23, 23, 31, 31, 31, 31, 31, 81, 81, 201, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 43, 44, 45, 46, 23, 24] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478466 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 152, 195, 129, 152, 65, 65, 65, 65, 48, 36, 48, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 152, 152, 152, 129, 129, 65, 65, 65, 65, 65, 36, 36, 1, 65, 65, 201, 201, 201, 201] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 770 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478466 none CSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 24, 10, 24, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 12, 19, 65, 65, 65, 65, 65, 1, 31, 31, 34, 34, 34, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 12, 12, 65, 1, 1, 31, 31, 31, 31] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478466 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478466 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478466/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478466 Building REAL300025478467 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478467' /scratch/stefan/7787258/working/building/REAL300025478467 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478467 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478467/0 /scratch/stefan/7787258/working/building/REAL300025478467 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/348 `/scratch/stefan/7787258/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOCC1) `REAL300025478467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478467 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 6, 6, 14, 20, 63, 63, 63, 63, 63, 1, 11, 20, 20, 35, 35, 35, 35, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478467 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 26, 35, 35, 35, 35, 63, 63, 108, 134, 201, 201, 201, 201, 201, 35, 1, 6, 1, 1, 1, 1, 1, 14, 14, 14, 26, 26, 35, 35, 35, 35, 35, 108, 108, 201, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 597 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478467 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 137, 63, 63, 63, 63, 49, 40, 49, 13, 1, 1, 1, 1, 1, 1, 1, 63, 159, 178, 178, 201, 201, 201, 201, 159, 159, 159, 137, 137, 63, 63, 63, 63, 63, 40, 40, 1, 63, 63, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478467 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478467 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478467/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478467 Building REAL300025478468 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478468' /scratch/stefan/7787258/working/building/REAL300025478468 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478468 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478468/0 /scratch/stefan/7787258/working/building/REAL300025478468 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/349 `/scratch/stefan/7787258/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CCO)CC1) `REAL300025478468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478468 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 17, 66, 66, 66, 66, 66, 1, 12, 21, 21, 21, 28, 37, 21, 21, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 66, 1, 1, 28, 28, 37, 37, 111, 21, 21, 21, 21] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 379 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: REAL300025478468 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 5, 13, 21, 21, 21, 21, 31, 31, 58, 91, 200, 200, 200, 200, 200, 21, 1, 3, 1, 1, 6, 10, 1, 1, 5, 5, 5, 13, 13, 21, 21, 21, 21, 21, 58, 58, 200, 21, 21, 6, 6, 10, 10, 30, 1, 1, 1, 1] 603 rigid atoms, others: [46, 47, 48, 49, 18, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 559 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: REAL300025478468 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(CCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [164, 132, 66, 66, 66, 66, 53, 31, 53, 13, 1, 1, 1, 1, 1, 1, 1, 66, 164, 200, 200, 200, 201, 201, 200, 200, 164, 164, 164, 132, 132, 66, 66, 66, 66, 66, 31, 31, 1, 66, 66, 201, 201, 201, 201, 603, 200, 200, 200, 200] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1354 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478468 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478468 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478468/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478468 Building REAL300025478469 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478469' /scratch/stefan/7787258/working/building/REAL300025478469 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478469 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478469/0 /scratch/stefan/7787258/working/building/REAL300025478469 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/350 `/scratch/stefan/7787258/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478469 none CC(C)C(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 32, 33, 25, 32, 32, 13, 25, 6, 13, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 67, 67, 67, 67, 67, 1, 33, 33, 33, 33, 33, 33, 33, 32, 32, 32, 96, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 11, 11, 67, 1, 1] 603 rigid atoms, others: [43, 44, 10, 11, 12, 13, 14, 45, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 333 number of broken/clashed sets: 240 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478469 none CC(C)C(C)(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 172, 201, 201, 163, 172, 137, 163, 67, 67, 67, 67, 51, 39, 51, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 603, 163, 163, 163, 137, 137, 67, 67, 67, 67, 67, 39, 39, 1, 67, 67] 603 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 1438 number of broken/clashed sets: 240 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478469 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478469 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478469/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478469 Building REAL300025478470 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478470' /scratch/stefan/7787258/working/building/REAL300025478470 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478470 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478470/0 /scratch/stefan/7787258/working/building/REAL300025478470 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/351 `/scratch/stefan/7787258/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC(C)(C)C1) `REAL300025478470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478470 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 4, 4, 11, 21, 68, 68, 68, 68, 68, 1, 16, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 11, 11, 68, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 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: REAL300025478470 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 8, 17, 17, 17, 17, 30, 30, 56, 98, 201, 201, 201, 201, 201, 17, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 56, 56, 201, 17, 17, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [54, 45, 46, 18, 20, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 494 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: REAL300025478470 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 154, 68, 68, 68, 68, 50, 31, 50, 13, 1, 1, 1, 1, 1, 1, 1, 68, 197, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 154, 154, 68, 68, 68, 68, 68, 31, 31, 1, 68, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 768 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478470 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478470 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478470/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478470 Building REAL300025478471 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478471' /scratch/stefan/7787258/working/building/REAL300025478471 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478471 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478471/0 /scratch/stefan/7787258/working/building/REAL300025478471 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/352 `/scratch/stefan/7787258/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCSC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478471 none CC1CCSC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 14, 26, 26, 26, 26, 44, 44, 80, 113, 201, 201, 201, 201, 201, 26, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 26, 26, 26, 26, 26, 80, 80, 201, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478471 none CC1CCSC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 193, 201, 168, 193, 85, 85, 85, 85, 58, 46, 58, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 168, 168, 85, 85, 85, 85, 85, 46, 46, 1, 85, 85] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 747 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478471 none CC1CCSC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 17, 14, 17, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 85, 85, 85, 85, 85, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 85, 1, 1] 201 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478471 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478471 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478471/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478471 Building REAL300025478472 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478472' /scratch/stefan/7787258/working/building/REAL300025478472 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478472 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478472/0 /scratch/stefan/7787258/working/building/REAL300025478472 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/353 `/scratch/stefan/7787258/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478472 none CC(C[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 15, 19, 19, 19, 19, 8, 11, 6, 8, 1, 1, 1, 1, 1, 1, 5, 5, 10, 12, 30, 30, 30, 30, 30, 1, 15, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 10, 10, 30, 1, 1] 41 rigid atoms, others: [16, 47, 12, 11, 44, 13, 14, 45, 48, 52, 46, 26, 15, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51]) total number of confs: 141 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478472 none CC(C[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 40, 41, 41, 41, 41, 41, 38, 40, 35, 38, 30, 30, 30, 30, 29, 26, 29, 13, 1, 1, 1, 1, 1, 1, 1, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 38, 38, 38, 35, 35, 30, 30, 30, 30, 30, 26, 26, 1, 30, 30] 41 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 153 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478472 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478472 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478472/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478472 Building REAL300025478473 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478473' /scratch/stefan/7787258/working/building/REAL300025478473 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478473 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478473/0 /scratch/stefan/7787258/working/building/REAL300025478473 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/354 `/scratch/stefan/7787258/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN(C)N=N1) `REAL300025478473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478473 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 5, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 72, 72, 72, 72, 72, 1, 13, 24, 24, 33, 37, 37, 37, 37, 37, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1, 33, 33, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 253 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478473 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 5, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 13, 18, 29, 37, 37, 37, 37, 47, 47, 81, 114, 201, 201, 201, 201, 201, 37, 6, 13, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 29, 29, 37, 37, 37, 37, 37, 81, 81, 201, 37, 37, 6, 6, 1, 2, 2, 2] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 561 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478473 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 5, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 117, 72, 72, 72, 72, 50, 41, 50, 12, 1, 1, 1, 1, 1, 1, 1, 72, 170, 193, 193, 199, 201, 201, 201, 201, 201, 170, 170, 170, 117, 117, 72, 72, 72, 72, 72, 41, 41, 1, 72, 72, 199, 199, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 752 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478473 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478473 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478473/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478473 Building REAL300025478474 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478474' /scratch/stefan/7787258/working/building/REAL300025478474 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478474 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478474/0 /scratch/stefan/7787258/working/building/REAL300025478474 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/355 `/scratch/stefan/7787258/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN=CS1) `REAL300025478474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478474 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 58, 58, 58, 58, 58, 1, 10, 25, 25, 29, 29, 29, 29, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 58, 1, 1, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478474 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 24, 29, 29, 29, 29, 46, 46, 85, 117, 201, 201, 201, 201, 201, 29, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 29, 29, 29, 29, 29, 85, 85, 201, 29, 29, 1] 201 rigid atoms, others: [40, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 548 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478474 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 114, 58, 58, 58, 58, 43, 37, 43, 13, 1, 1, 1, 1, 1, 1, 1, 58, 139, 195, 195, 201, 201, 201, 201, 139, 139, 139, 114, 114, 58, 58, 58, 58, 58, 37, 37, 1, 58, 58, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478474 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478474 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478474/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478474 Building REAL300025478475 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478475' /scratch/stefan/7787258/working/building/REAL300025478475 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478475 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478475/0 /scratch/stefan/7787258/working/building/REAL300025478475 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/356 `/scratch/stefan/7787258/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1[C@H]2CCCO[C@H]21) `REAL300025478475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478475 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1[C@H]2CCCO[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 14, 22, 55, 55, 55, 55, 55, 1, 14, 25, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 7, 44, 17, 35, 43, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 230 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: REAL300025478475 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1[C@H]2CCCO[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 24, 39, 39, 39, 39, 58, 58, 98, 127, 201, 201, 201, 201, 201, 39, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 39, 39, 39, 39, 39, 98, 98, 201, 39, 39, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 565 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: REAL300025478475 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1[C@H]2CCCO[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 123, 55, 55, 55, 55, 37, 30, 37, 13, 1, 1, 1, 1, 1, 1, 1, 55, 141, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 141, 123, 123, 55, 55, 55, 55, 55, 30, 30, 1, 55, 55, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 756 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478475 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478475 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478475/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478475 Building REAL300025478476 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478476' /scratch/stefan/7787258/working/building/REAL300025478476 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478476 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478476/0 /scratch/stefan/7787258/working/building/REAL300025478476 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/357 `/scratch/stefan/7787258/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=C1) `REAL300025478476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478476 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 18, 29, 29, 29, 29, 49, 49, 85, 116, 201, 201, 201, 201, 201, 29, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 18, 29, 29, 29, 29, 29, 85, 85, 201, 29, 29, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478476 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 169, 161, 169, 147, 161, 70, 70, 70, 70, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 161, 161, 161, 147, 147, 70, 70, 70, 70, 70, 42, 42, 1, 70, 70, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 715 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478476 none CC1=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 13, 18, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 70, 70, 70, 70, 70, 1, 29, 29, 29, 29, 29, 29, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 13, 13, 70, 1, 1, 29] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 43, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478476 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478476 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478476/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478476 Building REAL300025478477 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478477' /scratch/stefan/7787258/working/building/REAL300025478477 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478477 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478477/0 /scratch/stefan/7787258/working/building/REAL300025478477 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/358 `/scratch/stefan/7787258/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C1CCC1) `REAL300025478477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478477 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 17, 53, 53, 53, 53, 53, 1, 10, 17, 17, 17, 17, 30, 30, 30, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 12, 12, 53, 1, 1, 17, 30, 30, 30, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 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: REAL300025478477 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 22, 30, 30, 30, 30, 49, 49, 87, 110, 201, 201, 201, 201, 201, 30, 5, 8, 1, 5, 1, 1, 1, 1, 10, 10, 10, 22, 22, 30, 30, 30, 30, 30, 87, 87, 201, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 20, 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, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 567 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: REAL300025478477 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 103, 53, 53, 53, 53, 43, 36, 43, 13, 1, 1, 1, 1, 1, 1, 1, 53, 116, 135, 135, 135, 135, 201, 201, 201, 116, 116, 116, 103, 103, 53, 53, 53, 53, 53, 36, 36, 1, 53, 53, 135, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 787 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478477 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478477 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478477/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478477 Building REAL300025478478 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478478' /scratch/stefan/7787258/working/building/REAL300025478478 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478478 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478478/0 /scratch/stefan/7787258/working/building/REAL300025478478 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/359 `/scratch/stefan/7787258/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC(F)F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478478 none CC(OC(F)F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 16, 28, 33, 36, 36, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 5, 5, 16, 28, 79, 79, 79, 79, 79, 1, 28, 28, 28, 28, 36, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 16, 16, 79, 1, 1] 201 rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 271 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: REAL300025478478 none CC(OC(F)F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 189, 200, 201, 201, 201, 189, 189, 171, 189, 79, 79, 79, 79, 52, 43, 52, 13, 1, 1, 1, 1, 1, 1, 1, 79, 200, 200, 200, 200, 201, 189, 189, 189, 171, 171, 79, 79, 79, 79, 79, 43, 43, 1, 79, 79] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 795 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478478 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478478 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478478/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478478 Building REAL300025478479 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478479' /scratch/stefan/7787258/working/building/REAL300025478479 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478479 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478479/0 /scratch/stefan/7787258/working/building/REAL300025478479 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/360 `/scratch/stefan/7787258/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(C)O1) `REAL300025478479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478479 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 13, 21, 61, 61, 61, 61, 61, 1, 12, 23, 23, 24, 24, 24, 24, 24, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 61, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478479 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 15, 24, 24, 24, 24, 41, 41, 72, 104, 201, 201, 201, 201, 201, 24, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 24, 24, 24, 24, 24, 72, 72, 201, 24, 24, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478479 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 125, 61, 61, 61, 61, 44, 38, 44, 13, 1, 1, 1, 1, 1, 1, 1, 61, 156, 199, 199, 201, 201, 201, 201, 201, 156, 156, 156, 125, 125, 61, 61, 61, 61, 61, 38, 38, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478479 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478479 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478479/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478479 Building REAL300025478480 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478480' /scratch/stefan/7787258/working/building/REAL300025478480 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478480 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478480/0 /scratch/stefan/7787258/working/building/REAL300025478480 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/361 `/scratch/stefan/7787258/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478480 none C#CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 19, 36, 36, 36, 36, 53, 53, 94, 124, 201, 201, 201, 201, 201, 36, 1, 1, 1, 1, 8, 8, 8, 19, 19, 36, 36, 36, 36, 36, 94, 94, 201, 36, 36] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478480 none C#CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 178, 177, 178, 145, 177, 69, 69, 69, 69, 48, 38, 48, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 177, 177, 177, 145, 145, 69, 69, 69, 69, 69, 38, 38, 1, 69, 69] 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, 43, 44]) total number of confs: 728 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478480 none C#CC1=CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 17, 14, 17, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 69, 69, 69, 69, 69, 1, 36, 36, 36, 36, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 13, 13, 69, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 43, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478480 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478480 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478480/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478480 Building REAL300025478481 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478481' /scratch/stefan/7787258/working/building/REAL300025478481 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478481 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478481/0 /scratch/stefan/7787258/working/building/REAL300025478481 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/362 `/scratch/stefan/7787258/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1) `REAL300025478481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478481 none CC1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 12, 12, 24, 34, 34, 34, 34, 52, 52, 96, 126, 201, 201, 201, 201, 201, 34, 1, 1, 2, 2, 2, 1, 1, 1, 12, 12, 12, 24, 24, 34, 34, 34, 34, 34, 96, 96, 201, 34, 34] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478481 none CC1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 181, 176, 181, 143, 176, 72, 72, 72, 72, 57, 44, 57, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 143, 143, 72, 72, 72, 72, 72, 44, 44, 1, 72, 72] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 740 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478481 none CC1CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 16, 11, 16, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 15, 23, 72, 72, 72, 72, 72, 1, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 15, 72, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478481 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478481 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478481/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478481 Building REAL300025478482 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478482' /scratch/stefan/7787258/working/building/REAL300025478482 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478482 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478482/0 /scratch/stefan/7787258/working/building/REAL300025478482 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/363 `/scratch/stefan/7787258/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(C)(C)N=[N+]=[N-]) `REAL300025478482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478482 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(C)(C)N=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 51, 51, 51, 51, 51, 1, 12, 20, 20, 22, 29, 29, 29, 41, 41, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 14, 14, 51, 1, 1, 22, 22, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 237 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478482 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(C)(C)N=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 87, 51, 51, 51, 51, 40, 36, 40, 13, 1, 1, 1, 1, 1, 1, 1, 51, 102, 130, 130, 141, 173, 173, 173, 201, 201, 102, 102, 102, 87, 87, 51, 51, 51, 51, 51, 36, 36, 1, 51, 51, 141, 141, 173, 173, 173, 173, 173, 173] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 783 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478482 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478482 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478482/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478482 Building REAL300025478483 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478483' /scratch/stefan/7787258/working/building/REAL300025478483 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478483 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478483/0 /scratch/stefan/7787258/working/building/REAL300025478483 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/364 `/scratch/stefan/7787258/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(F)C1) `REAL300025478483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478483 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 55, 55, 55, 55, 55, 1, 14, 29, 29, 38, 38, 38, 38, 38, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 14, 55, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478483 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 27, 38, 38, 38, 38, 53, 53, 93, 120, 201, 201, 201, 201, 201, 38, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 27, 27, 38, 38, 38, 38, 38, 93, 93, 201, 38, 38, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [41, 42, 43, 47, 48, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478483 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 111, 55, 55, 55, 55, 40, 34, 40, 13, 1, 1, 1, 1, 1, 1, 1, 55, 126, 168, 168, 201, 201, 201, 201, 201, 126, 126, 126, 111, 111, 55, 55, 55, 55, 55, 34, 34, 1, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478483 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478483 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478483/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478483 Building REAL300025478484 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478484' /scratch/stefan/7787258/working/building/REAL300025478484 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478484 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478484/0 /scratch/stefan/7787258/working/building/REAL300025478484 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/365 `/scratch/stefan/7787258/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(=O)NC1CC1) `REAL300025478484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478484 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 14, 44, 44, 44, 44, 44, 1, 6, 10, 10, 10, 15, 15, 15, 31, 31, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 10, 10, 44, 1, 1, 10, 10, 15, 31, 31, 31, 31, 31] 90 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478484 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 30, 31, 31, 31, 31, 39, 39, 49, 62, 90, 90, 90, 90, 90, 31, 14, 23, 6, 6, 6, 1, 1, 1, 1, 23, 23, 23, 30, 30, 31, 31, 31, 31, 31, 49, 49, 90, 31, 31, 14, 14, 6, 1, 1, 1, 1, 1] 90 rigid atoms, others: [45, 46, 47, 48, 49, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478484 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [60, 59, 44, 44, 44, 44, 42, 36, 42, 13, 1, 1, 1, 1, 1, 1, 1, 44, 60, 68, 68, 68, 80, 80, 80, 90, 90, 60, 60, 60, 59, 59, 44, 44, 44, 44, 44, 36, 36, 1, 44, 44, 68, 68, 80, 90, 90, 90, 90, 90] 90 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478484 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478484 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478484/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478484 Building REAL300025478485 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478485' /scratch/stefan/7787258/working/building/REAL300025478485 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478485 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478485/0 /scratch/stefan/7787258/working/building/REAL300025478485 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/366 `/scratch/stefan/7787258/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478485 none COCC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 32, 23, 10, 23, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 68, 68, 68, 68, 68, 1, 46, 46, 46, 32, 32, 23, 69, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 68, 1, 1] 603 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 360 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478485 none COCC(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 195, 135, 195, 135, 135, 120, 135, 68, 68, 68, 68, 46, 39, 46, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 195, 585, 135, 135, 135, 120, 120, 68, 68, 68, 68, 68, 39, 39, 1, 68, 68] 603 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 1469 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478485 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478485 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478485/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478485 Building REAL300025478486 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478486' /scratch/stefan/7787258/working/building/REAL300025478486 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478486 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478486/0 /scratch/stefan/7787258/working/building/REAL300025478486 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/367 `/scratch/stefan/7787258/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1) `REAL300025478486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478486 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 16, 27, 27, 27, 27, 49, 49, 85, 113, 201, 201, 201, 201, 201, 27, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 27, 27, 27, 27, 27, 85, 85, 201, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478486 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 181, 183, 152, 181, 73, 73, 73, 73, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 152, 152, 73, 73, 73, 73, 73, 39, 39, 1, 73, 73] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 769 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478486 none CC1CCC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 17, 13, 17, 5, 13, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 73, 73, 73, 73, 73, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 73, 1, 1] 201 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478486 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478486 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478486/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478486 Building REAL300025478487 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478487' /scratch/stefan/7787258/working/building/REAL300025478487 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478487 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478487/0 /scratch/stefan/7787258/working/building/REAL300025478487 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/368 `/scratch/stefan/7787258/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478487 none C#CC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 14, 20, 5, 14, 1, 1, 1, 1, 1, 1, 2, 2, 6, 11, 57, 57, 57, 57, 57, 1, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 6, 6, 57, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 45, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 153 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: REAL300025478487 none C#CC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 152, 201, 123, 152, 57, 57, 57, 57, 40, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 123, 123, 57, 57, 57, 57, 57, 29, 29, 1, 57, 57] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 773 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478487 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478487 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478487/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478487 Building REAL300025478488 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478488' /scratch/stefan/7787258/working/building/REAL300025478488 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478488 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478488/0 /scratch/stefan/7787258/working/building/REAL300025478488 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/369 `/scratch/stefan/7787258/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCOC1) `REAL300025478488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478488 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 68, 68, 68, 68, 68, 1, 11, 18, 18, 34, 34, 41, 41, 41, 41, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 14, 14, 68, 1, 1, 34, 34, 41, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 259 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: REAL300025478488 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 33, 41, 41, 41, 41, 60, 60, 96, 126, 201, 201, 201, 201, 201, 41, 5, 16, 5, 1, 1, 1, 1, 1, 1, 20, 20, 20, 33, 33, 41, 41, 41, 41, 41, 96, 96, 201, 41, 41, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 565 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: REAL300025478488 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 68, 68, 68, 68, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 68, 141, 168, 168, 200, 200, 201, 201, 201, 201, 141, 141, 141, 125, 125, 68, 68, 68, 68, 68, 41, 41, 1, 68, 68, 200, 200, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 771 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478488 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478488 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478488/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478488 Building REAL300025478489 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478489' /scratch/stefan/7787258/working/building/REAL300025478489 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478489 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478489/0 /scratch/stefan/7787258/working/building/REAL300025478489 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/370 `/scratch/stefan/7787258/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478489 none COC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 27, 37, 13, 27, 11, 13, 5, 11, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 70, 70, 70, 70, 70, 1, 37, 37, 37, 37, 37, 37, 37, 27, 81, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 70, 1, 1] 603 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 44, 48, 49, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 361 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478489 none COC(C)C(O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 197, 201, 183, 197, 180, 183, 139, 180, 70, 70, 70, 70, 49, 36, 49, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 201, 197, 591, 180, 180, 180, 139, 139, 70, 70, 70, 70, 70, 36, 36, 1, 70, 70] 603 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 1384 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478489 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478489 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478489/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478489 Building REAL300025478490 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478490' /scratch/stefan/7787258/working/building/REAL300025478490 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478490 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478490/0 /scratch/stefan/7787258/working/building/REAL300025478490 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/371 `/scratch/stefan/7787258/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CNC(=O)N1) `REAL300025478490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478490 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 15, 21, 53, 53, 53, 53, 53, 1, 14, 31, 31, 48, 48, 48, 48, 48, 48, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 15, 15, 53, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 252 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478490 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 36, 48, 48, 48, 48, 79, 79, 125, 149, 201, 201, 201, 201, 201, 48, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 36, 36, 48, 48, 48, 48, 48, 125, 125, 201, 48, 48, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 642 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478490 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 107, 53, 53, 53, 53, 41, 35, 41, 13, 1, 1, 1, 1, 1, 1, 1, 53, 142, 178, 178, 201, 201, 201, 201, 201, 201, 142, 142, 142, 107, 107, 53, 53, 53, 53, 53, 35, 35, 1, 53, 53, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 766 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478490 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478490 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478490/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478490 Building REAL300025478491 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478491' /scratch/stefan/7787258/working/building/REAL300025478491 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478491 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478491/0 /scratch/stefan/7787258/working/building/REAL300025478491 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/372 `/scratch/stefan/7787258/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478491 none CCSC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 17, 14, 17, 13, 14, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 66, 66, 66, 66, 66, 1, 32, 32, 32, 32, 32, 17, 17, 17, 17, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 14, 14, 66, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 216 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: REAL300025478491 none CCSC(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 174, 173, 174, 169, 173, 148, 169, 66, 66, 66, 66, 50, 38, 50, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 174, 174, 174, 174, 169, 169, 169, 148, 148, 66, 66, 66, 66, 66, 38, 38, 1, 66, 66] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 725 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478491 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478491 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478491/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478491 Building REAL300025478492 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478492' /scratch/stefan/7787258/working/building/REAL300025478492 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478492 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478492/0 /scratch/stefan/7787258/working/building/REAL300025478492 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/373 `/scratch/stefan/7787258/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+]1CC(C)C1) `REAL300025478492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 6, 8, 12, 12, 12, 12, 12, 1, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 6, 6, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 12 rigid atoms, others: [11, 37, 6, 7, 8, 9, 10, 39, 45, 46, 40, 21, 41, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 57 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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 5, 6, 6, 7, 7, 7, 7, 7, 8, 8, 12, 12, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1] 12 rigid atoms, others: [1, 54, 47, 48, 49, 53, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 59 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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+]1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [44, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 31 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478492 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478492/1 /scratch/stefan/7787258/working/building/REAL300025478492 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/374 `/scratch/stefan/7787258/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CC(C)C1) `REAL300025478492.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 16, 19, 6, 16, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 93, 93, 93, 93, 93, 1, 27, 33, 33, 33, 33, 27, 27, 27, 27, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 14, 14, 93, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 44, 45, 40, 21, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 269 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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 5, 8, 8, 18, 33, 33, 33, 33, 55, 55, 100, 126, 201, 201, 201, 201, 201, 33, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 8, 8, 18, 18, 33, 33, 33, 33, 33, 100, 100, 201, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 52, 53, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51]) total number of confs: 585 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: REAL300025478492 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 192, 200, 176, 192, 93, 93, 93, 93, 63, 48, 63, 13, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 176, 176, 93, 93, 93, 93, 93, 48, 48, 1, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 772 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478492 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478492 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478492/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478492/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478492 Building REAL300025478493 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478493' /scratch/stefan/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478493 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478493/0 /scratch/stefan/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/375 `/scratch/stefan/7787258/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478493 none CC1CCN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 11, 11, 19, 29, 29, 29, 29, 44, 44, 80, 112, 201, 201, 201, 201, 201, 29, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 19, 19, 29, 29, 29, 29, 29, 80, 80, 201, 29, 29] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CCN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 197, 193, 197, 167, 193, 80, 80, 80, 80, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 167, 167, 80, 80, 80, 80, 80, 41, 41, 1, 80, 80] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 768 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CCN1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 20, 14, 20, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 80, 80, 80, 80, 80, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 14, 14, 80, 1, 1] 201 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 44, 49, 50, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478493/1 /scratch/stefan/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/376 `/scratch/stefan/7787258/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478493.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478493 none CC1CC[N@@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 6, 7, 7, 7, 7, 8, 8, 13, 13, 15, 15, 15, 15, 15, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 7, 13, 13, 15, 7, 7] 15 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CC[N@@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 15, 12, 12, 12, 12, 12, 12, 12, 11, 1, 1, 1, 1, 1, 1, 1, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 15 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CC[N@@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 12, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1] 15 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478493/2 /scratch/stefan/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/377 `/scratch/stefan/7787258/working/3D/377' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478493.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CC[N@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 6, 7, 7, 7, 7, 8, 8, 13, 13, 15, 15, 15, 15, 15, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 7, 13, 13, 15, 7, 7] 15 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 5, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CC[N@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 15, 12, 12, 12, 12, 12, 12, 12, 11, 1, 1, 1, 1, 1, 1, 1, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 15 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478493 none CC1CC[N@H+]1CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 12, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1] 15 rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/7787258/working/building/REAL300025478493 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478493 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478493/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478493/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478493/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478493 Building REAL300025478494 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478494' /scratch/stefan/7787258/working/building/REAL300025478494 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478494 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478494/0 /scratch/stefan/7787258/working/building/REAL300025478494 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/378 `/scratch/stefan/7787258/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478494 none COC(C)(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 23, 11, 22, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 76, 76, 76, 76, 76, 1, 23, 26, 26, 23, 23, 23, 23, 23, 23, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 13, 13, 76, 1, 1, 26, 26, 26, 26, 26] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 46, 47, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 221 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: REAL300025478494 none COC(C)(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 4, 6, 6, 7, 7, 16, 26, 26, 26, 26, 39, 39, 73, 106, 201, 201, 201, 201, 201, 26, 1, 1, 1, 6, 6, 6, 4, 4, 4, 7, 7, 7, 16, 16, 26, 26, 26, 26, 26, 73, 73, 201, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 530 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: REAL300025478494 none COC(C)(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 174, 200, 133, 174, 76, 76, 76, 76, 50, 39, 50, 13, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 133, 133, 76, 76, 76, 76, 76, 39, 39, 1, 76, 76, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 774 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478494 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478494 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478494/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478494 Building REAL300025478495 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478495' /scratch/stefan/7787258/working/building/REAL300025478495 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478495 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478495/0 /scratch/stefan/7787258/working/building/REAL300025478495 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/379 `/scratch/stefan/7787258/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1CC1) `REAL300025478495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478495 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 45, 45, 45, 45, 45, 1, 9, 11, 11, 15, 25, 37, 37, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 9, 9, 45, 1, 1, 15, 15, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478495 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 22, 31, 37, 37, 37, 37, 53, 53, 81, 110, 201, 201, 201, 201, 201, 37, 15, 21, 6, 1, 1, 1, 1, 22, 22, 22, 31, 31, 37, 37, 37, 37, 37, 81, 81, 201, 37, 37, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 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, 40, 41]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478495 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 90, 45, 45, 45, 45, 36, 31, 36, 13, 1, 1, 1, 1, 1, 1, 1, 45, 101, 102, 102, 134, 173, 201, 201, 101, 101, 101, 90, 90, 45, 45, 45, 45, 45, 31, 31, 1, 45, 45, 134, 134, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478495 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478495 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478495/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478495 Building REAL300025478496 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478496' /scratch/stefan/7787258/working/building/REAL300025478496 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478496 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478496/0 /scratch/stefan/7787258/working/building/REAL300025478496 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/380 `/scratch/stefan/7787258/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1) `REAL300025478496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478496 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 71, 71, 71, 71, 71, 1, 13, 25, 25, 27, 27, 27, 27, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 8, 8, 71, 1, 1, 27, 27, 27] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478496 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 20, 30, 30, 30, 30, 45, 45, 76, 103, 201, 201, 201, 201, 201, 30, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 30, 30, 30, 30, 30, 76, 76, 201, 30, 30, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478496 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 142, 71, 71, 71, 71, 49, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 71, 174, 201, 201, 201, 201, 201, 201, 174, 174, 174, 142, 142, 71, 71, 71, 71, 71, 31, 31, 1, 71, 71, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478496 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478496 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478496/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478496 Building REAL300025478497 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478497' /scratch/stefan/7787258/working/building/REAL300025478497 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478497 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478497/0 /scratch/stefan/7787258/working/building/REAL300025478497 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/381 `/scratch/stefan/7787258/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCC1) `REAL300025478497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478497 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 9, 13, 41, 41, 41, 41, 41, 1, 8, 13, 13, 21, 21, 53, 53, 53, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 9, 9, 41, 1, 1, 21, 21, 53, 53, 53, 53, 53, 53, 53] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 242 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: REAL300025478497 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 43, 53, 53, 53, 53, 79, 79, 100, 132, 201, 201, 201, 201, 201, 53, 7, 23, 7, 1, 1, 1, 1, 1, 23, 23, 23, 43, 43, 53, 53, 53, 53, 53, 100, 100, 201, 53, 53, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 587 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478497 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 74, 41, 41, 41, 41, 38, 33, 38, 13, 1, 1, 1, 1, 1, 1, 1, 41, 95, 99, 99, 125, 125, 201, 201, 201, 95, 95, 95, 74, 74, 41, 41, 41, 41, 41, 33, 33, 1, 41, 41, 125, 125, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 792 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478497 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478497 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478497/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478497 Building REAL300025478498 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478498' /scratch/stefan/7787258/working/building/REAL300025478498 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478498 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478498/0 /scratch/stefan/7787258/working/building/REAL300025478498 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/382 `/scratch/stefan/7787258/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1) `REAL300025478498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478498 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 3, 3, 5, 5, 17, 29, 29, 29, 29, 44, 44, 76, 103, 201, 201, 201, 201, 201, 29, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 17, 17, 29, 29, 29, 29, 29, 76, 76, 201, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 535 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478498 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 132, 195, 118, 132, 54, 54, 54, 54, 39, 33, 39, 12, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 118, 118, 54, 54, 54, 54, 54, 33, 33, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 788 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478498 none COC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 23, 12, 23, 6, 12, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 54, 54, 54, 54, 54, 1, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 9, 9, 54, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478498 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478498 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478498/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478498 Building REAL300025478499 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478499' /scratch/stefan/7787258/working/building/REAL300025478499 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478499 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478499/0 /scratch/stefan/7787258/working/building/REAL300025478499 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/383 `/scratch/stefan/7787258/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NN1C) `REAL300025478499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478499 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 7, 7, 13, 23, 67, 67, 67, 67, 67, 1, 15, 30, 30, 40, 40, 40, 40, 40, 40, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 13, 13, 67, 1, 1, 40, 40, 40, 40, 40] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478499 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 28, 40, 40, 40, 40, 57, 57, 101, 126, 201, 201, 201, 201, 201, 40, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 28, 40, 40, 40, 40, 40, 101, 101, 201, 40, 40, 1, 1, 2, 2, 2] 201 rigid atoms, others: [42, 43, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 604 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: REAL300025478499 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)NN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 136, 67, 67, 67, 67, 53, 41, 53, 13, 1, 1, 1, 1, 1, 1, 1, 67, 145, 176, 176, 201, 201, 201, 201, 201, 201, 145, 145, 145, 136, 136, 67, 67, 67, 67, 67, 41, 41, 1, 67, 67, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 726 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478499 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478499 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478499/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478499 Building REAL300025478500 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478500' /scratch/stefan/7787258/working/building/REAL300025478500 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478500 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478500/0 /scratch/stefan/7787258/working/building/REAL300025478500 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/384 `/scratch/stefan/7787258/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478500 none CCC1=CNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 10, 10, 18, 28, 28, 28, 28, 30, 30, 60, 72, 135, 135, 135, 135, 135, 28, 1, 3, 4, 3, 3, 3, 1, 1, 10, 10, 10, 18, 18, 28, 28, 28, 28, 28, 60, 60, 135, 28, 28, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 49, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 373 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: REAL300025478500 none CCC1=CNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 135, 135, 135, 135, 100, 99, 100, 77, 99, 47, 47, 47, 47, 47, 38, 47, 13, 1, 1, 1, 1, 1, 1, 1, 47, 135, 201, 201, 201, 201, 201, 135, 135, 99, 99, 99, 77, 77, 47, 47, 47, 47, 47, 38, 38, 1, 47, 47, 135] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 859 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: REAL300025478500 none CCC1=CNC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 12, 10, 12, 5, 10, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 47, 47, 47, 47, 47, 1, 28, 49, 49, 49, 49, 49, 28, 28, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 7, 7, 47, 1, 1, 28] 201 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 48, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49]) total number of confs: 258 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478500 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478500 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478500/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478500 Building REAL300025478501 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478501' /scratch/stefan/7787258/working/building/REAL300025478501 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478501 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478501/0 /scratch/stefan/7787258/working/building/REAL300025478501 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/385 `/scratch/stefan/7787258/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478501 none CCCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 24, 24, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 15, 23, 65, 65, 65, 65, 65, 1, 37, 37, 37, 37, 37, 37, 37, 24, 24, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 15, 65, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478501 none CCCC=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 132, 108, 108, 108, 105, 108, 65, 65, 65, 65, 51, 40, 51, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 132, 132, 108, 108, 108, 105, 105, 65, 65, 65, 65, 65, 40, 40, 1, 65, 65] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 902 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478501 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478501 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478501/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478501 Building REAL300025478502 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478502' /scratch/stefan/7787258/working/building/REAL300025478502 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478502 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478502/0 /scratch/stefan/7787258/working/building/REAL300025478502 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/386 `/scratch/stefan/7787258/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478502 none CC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 35, 12, 14, 6, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 80, 80, 80, 80, 80, 1, 35, 35, 35, 35, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 14, 14, 80, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478502 none CC=C(F)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 201, 190, 192, 160, 190, 80, 80, 80, 80, 56, 40, 56, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 190, 190, 190, 160, 160, 80, 80, 80, 80, 80, 40, 40, 1, 80, 80] 201 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478502 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478502 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478502/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478502 Building REAL300025478503 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478503' /scratch/stefan/7787258/working/building/REAL300025478503 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478503 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478503/0 /scratch/stefan/7787258/working/building/REAL300025478503 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/387 `/scratch/stefan/7787258/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NSNC1=O) `REAL300025478503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478503 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NSNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 14, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 59, 59, 59, 59, 59, 1, 13, 21, 21, 37, 37, 37, 37, 37, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 13, 13, 59, 1, 1, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478503 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NSNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 14, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 28, 37, 37, 37, 37, 53, 53, 91, 121, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 28, 28, 37, 37, 37, 37, 37, 91, 91, 201, 37, 37, 1] 201 rigid atoms, others: [41, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478503 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=NSNC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 8, 14, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 109, 59, 59, 59, 59, 44, 37, 44, 13, 1, 1, 1, 1, 1, 1, 1, 59, 127, 153, 153, 201, 201, 201, 201, 201, 127, 127, 127, 109, 109, 59, 59, 59, 59, 59, 37, 37, 1, 59, 59, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478503 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478503 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478503/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478503 Building REAL300025478504 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478504' /scratch/stefan/7787258/working/building/REAL300025478504 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478504 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478504/0 /scratch/stefan/7787258/working/building/REAL300025478504 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/388 `/scratch/stefan/7787258/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025478504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478504 none CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 13, 12, 13, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 18, 28, 86, 86, 86, 86, 86, 1, 18, 21, 21, 18, 18, 18, 18, 18, 18, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 18, 18, 86, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 45, 46, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 249 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: REAL300025478504 none CCC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 195, 196, 178, 195, 86, 86, 86, 86, 56, 41, 56, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 178, 178, 86, 86, 86, 86, 86, 41, 41, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 767 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478504 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478504 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478504/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478504 Building REAL300025478505 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478505' /scratch/stefan/7787258/working/building/REAL300025478505 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478505 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478505/0 /scratch/stefan/7787258/working/building/REAL300025478505 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/389 `/scratch/stefan/7787258/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478505 none CSC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 18, 18, 18, 11, 18, 5, 11, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 51, 51, 51, 51, 51, 1, 26, 26, 26, 18, 18, 18, 18, 18, 18, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 9, 9, 51, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 166 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: REAL300025478505 none CSC(C)(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 195, 195, 142, 195, 114, 142, 51, 51, 51, 51, 35, 31, 35, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 195, 195, 195, 195, 195, 195, 142, 142, 142, 114, 114, 51, 51, 51, 51, 51, 31, 31, 1, 51, 51] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 765 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478505 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478505 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478505/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478505 Building REAL300025478506 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478506' /scratch/stefan/7787258/working/building/REAL300025478506 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478506 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478506/0 /scratch/stefan/7787258/working/building/REAL300025478506 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/390 `/scratch/stefan/7787258/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NS1) `REAL300025478506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478506 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 13, 39, 39, 39, 39, 39, 1, 13, 25, 25, 30, 48, 48, 48, 48, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 39, 1, 1, 30, 30, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 217 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: REAL300025478506 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 14, 34, 48, 48, 48, 48, 60, 60, 115, 137, 201, 201, 201, 201, 201, 48, 2, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 34, 34, 48, 48, 48, 48, 48, 115, 115, 201, 48, 48, 2, 2, 1] 201 rigid atoms, others: [43, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 639 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: REAL300025478506 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1=CN=NS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 8, 8, 14, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 80, 39, 39, 39, 39, 36, 32, 36, 13, 1, 1, 1, 1, 1, 1, 1, 39, 102, 133, 133, 136, 201, 201, 201, 201, 102, 102, 102, 80, 80, 39, 39, 39, 39, 39, 32, 32, 1, 39, 39, 136, 136, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 664 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478506 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478506 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478506/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478506 Building REAL300025478507 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478507' /scratch/stefan/7787258/working/building/REAL300025478507 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478507 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478507/0 /scratch/stefan/7787258/working/building/REAL300025478507 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/391 `/scratch/stefan/7787258/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)=C1CCC1) `REAL300025478507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478507 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 15, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 42, 42, 42, 42, 42, 1, 13, 25, 25, 33, 33, 33, 33, 33, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 8, 8, 42, 1, 1, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478507 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 15, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 25, 33, 33, 33, 33, 46, 46, 81, 104, 201, 201, 201, 201, 201, 33, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 33, 33, 33, 33, 33, 81, 81, 201, 33, 33, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 555 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478507 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 15, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 101, 42, 42, 42, 42, 32, 28, 32, 11, 1, 1, 1, 1, 1, 1, 1, 42, 124, 179, 179, 201, 201, 201, 201, 201, 124, 124, 124, 101, 101, 42, 42, 42, 42, 42, 28, 28, 1, 42, 42, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478507 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478507 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478507/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478507 Building REAL300025478508 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478508' /scratch/stefan/7787258/working/building/REAL300025478508 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478508 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478508/0 /scratch/stefan/7787258/working/building/REAL300025478508 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/392 `/scratch/stefan/7787258/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478508 none CCC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 25, 15, 25, 42, 14, 15, 7, 14, 1, 1, 1, 1, 1, 1, 5, 5, 16, 25, 87, 87, 87, 87, 87, 1, 27, 27, 27, 27, 27, 25, 42, 42, 126, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 16, 16, 87, 1, 1] 603 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 484 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478508 none CCC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [199, 201, 195, 201, 201, 193, 195, 173, 193, 87, 87, 87, 87, 62, 46, 62, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 603, 193, 193, 193, 173, 173, 87, 87, 87, 87, 87, 46, 46, 1, 87, 87] 603 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1390 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478508 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478508 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478508/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478508 Building REAL300025478509 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478509' /scratch/stefan/7787258/working/building/REAL300025478509 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478509 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478509/0 /scratch/stefan/7787258/working/building/REAL300025478509 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/393 `/scratch/stefan/7787258/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C(C)(C)O) `REAL300025478509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478509 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 70, 70, 70, 70, 70, 1, 10, 18, 18, 20, 20, 20, 20, 20, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 15, 15, 70, 1, 1, 20, 20, 20, 20, 20, 20, 20, 60] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 263 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478509 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C(F)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 15, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [174, 150, 70, 70, 70, 70, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 70, 174, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 150, 150, 70, 70, 70, 70, 70, 37, 37, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1382 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478509 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478509 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478509/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478509 Building REAL300025478510 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478510' /scratch/stefan/7787258/working/building/REAL300025478510 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478510 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478510/0 /scratch/stefan/7787258/working/building/REAL300025478510 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/394 `/scratch/stefan/7787258/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478510 none CC(C)CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 27, 22, 18, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 51, 51, 51, 51, 51, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 27, 27, 18, 18, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 51, 1, 1] 201 rigid atoms, others: [16, 15, 11, 12, 13, 14, 45, 48, 49, 46, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478510 none CC(C)CCOCC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 151, 142, 107, 107, 107, 95, 107, 51, 51, 51, 51, 40, 33, 40, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 142, 142, 107, 107, 107, 95, 95, 51, 51, 51, 51, 51, 33, 33, 1, 51, 51] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 909 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478510 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478510 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478510/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478510 Building REAL300025478511 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478511' /scratch/stefan/7787258/working/building/REAL300025478511 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478511 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478511/0 /scratch/stefan/7787258/working/building/REAL300025478511 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/395 `/scratch/stefan/7787258/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478511 none CC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 13, 26, 44, 11, 13, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 12, 22, 79, 79, 79, 79, 79, 1, 26, 26, 26, 26, 44, 44, 132, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 79, 1, 1] 603 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 460 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478511 none CC(CO)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 174, 201, 201, 173, 174, 148, 173, 79, 79, 79, 79, 61, 43, 61, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 603, 173, 173, 173, 148, 148, 79, 79, 79, 79, 79, 43, 43, 1, 79, 79] 603 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 1432 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478511 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478511 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478511/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478511 Building REAL300025478512 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478512' /scratch/stefan/7787258/working/building/REAL300025478512 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478512 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478512/0 /scratch/stefan/7787258/working/building/REAL300025478512 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/396 `/scratch/stefan/7787258/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CON=C1) `REAL300025478512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478512 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 28, 28, 28, 28, 28, 1, 9, 18, 18, 35, 35, 35, 35, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 28, 1, 1, 35, 35] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41]) total number of confs: 144 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: REAL300025478512 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 29, 35, 35, 35, 35, 43, 43, 66, 95, 201, 201, 201, 201, 201, 35, 1, 8, 1, 1, 1, 1, 1, 14, 14, 14, 29, 29, 35, 35, 35, 35, 35, 66, 66, 201, 35, 35, 1, 1] 201 rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 524 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: REAL300025478512 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 8, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 54, 28, 28, 28, 28, 19, 17, 19, 10, 1, 1, 1, 1, 1, 1, 1, 28, 71, 113, 113, 201, 201, 201, 201, 71, 71, 71, 54, 54, 28, 28, 28, 28, 28, 17, 17, 1, 28, 28, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 575 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478512 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478512 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478512/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478512 Building REAL300025478513 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478513' /scratch/stefan/7787258/working/building/REAL300025478513 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478513 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478513/0 /scratch/stefan/7787258/working/building/REAL300025478513 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/397 `/scratch/stefan/7787258/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNC=N1) `REAL300025478513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478513 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 50, 50, 50, 50, 50, 1, 11, 25, 25, 34, 34, 34, 34, 34, 34, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 10, 10, 50, 1, 1, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 199 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: REAL300025478513 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 25, 34, 34, 34, 34, 50, 50, 81, 105, 201, 201, 201, 201, 201, 34, 2, 6, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 34, 34, 34, 34, 34, 81, 81, 201, 34, 34, 2, 2, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 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]) total number of confs: 542 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478513 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 107, 50, 50, 50, 50, 36, 31, 36, 11, 1, 1, 1, 1, 1, 1, 1, 50, 124, 164, 164, 201, 201, 201, 201, 201, 201, 124, 124, 124, 107, 107, 50, 50, 50, 50, 50, 31, 31, 1, 50, 50, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 750 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478513 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478513 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478513/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478513 Building REAL300025478514 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478514' /scratch/stefan/7787258/working/building/REAL300025478514 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478514 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478514/0 /scratch/stefan/7787258/working/building/REAL300025478514 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/398 `/scratch/stefan/7787258/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1) `REAL300025478514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478514 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 3, 3, 6, 9, 25, 25, 25, 25, 25, 1, 5, 6, 6, 9, 9, 11, 11, 11, 11, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 6, 6, 25, 1, 1, 9, 9, 11, 11, 11] 31 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 80 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: REAL300025478514 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 7, 8, 8, 8, 8, 9, 9, 15, 21, 25, 25, 25, 25, 25, 8, 2, 5, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 15, 15, 25, 8, 8, 2, 2, 1, 1, 1] 25 rigid atoms, others: [44, 45, 46, 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]) total number of confs: 84 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478514 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 25, 25, 25, 25, 25, 23, 25, 12, 1, 1, 1, 1, 1, 1, 1, 25, 30, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 30, 30, 30, 25, 25, 25, 25, 25, 23, 23, 1, 25, 25, 31, 31, 31, 31, 31] 31 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478514 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478514 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478514/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478514 Building REAL300025478515 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478515' /scratch/stefan/7787258/working/building/REAL300025478515 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478515 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478515/0 /scratch/stefan/7787258/working/building/REAL300025478515 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/399 `/scratch/stefan/7787258/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1) `REAL300025478515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478515 none CCC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 4, 8, 8, 12, 12, 25, 40, 40, 40, 40, 55, 55, 95, 120, 201, 201, 201, 201, 201, 40, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 12, 12, 12, 25, 25, 40, 40, 40, 40, 40, 95, 95, 201, 40, 40, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 566 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: REAL300025478515 none CCC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 184, 160, 157, 160, 142, 157, 77, 77, 77, 77, 55, 41, 55, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 157, 157, 157, 142, 142, 77, 77, 77, 77, 77, 41, 41, 1, 77, 77, 201, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 827 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: REAL300025478515 none CCC1(CC(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 34, 17, 13, 17, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 77, 77, 77, 77, 77, 1, 40, 40, 40, 40, 40, 40, 40, 40, 34, 34, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 15, 15, 77, 1, 1, 40, 40, 40, 40] 201 rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 292 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478515 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478515 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478515/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478515 Building REAL300025478516 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478516' /scratch/stefan/7787258/working/building/REAL300025478516 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478516 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478516/0 /scratch/stefan/7787258/working/building/REAL300025478516 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/400 `/scratch/stefan/7787258/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNN=C1) `REAL300025478516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478516 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 21, 70, 70, 70, 70, 70, 1, 10, 18, 18, 30, 30, 53, 53, 53, 53, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 70, 1, 1, 30, 30, 53, 53, 53] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46]) 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: REAL300025478516 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 41, 50, 50, 50, 50, 72, 72, 102, 134, 201, 201, 201, 201, 201, 50, 6, 22, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 41, 41, 50, 50, 50, 50, 50, 102, 102, 201, 50, 50, 6, 6, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 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]) total number of confs: 585 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478516 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C=CC1=CNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 125, 70, 70, 70, 70, 57, 43, 57, 13, 1, 1, 1, 1, 1, 1, 1, 70, 146, 178, 178, 201, 201, 201, 201, 201, 201, 146, 146, 146, 125, 125, 70, 70, 70, 70, 70, 43, 43, 1, 70, 70, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 786 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478516 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478516 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478516/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478516 Building REAL300025478517 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478517' /scratch/stefan/7787258/working/building/REAL300025478517 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478517 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478517/0 /scratch/stefan/7787258/working/building/REAL300025478517 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/401 `/scratch/stefan/7787258/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@H]1CF) `REAL300025478517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478517 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 57, 57, 57, 57, 57, 1, 11, 18, 18, 27, 27, 27, 27, 27, 38, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 57, 1, 1, 27, 27, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 261 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478517 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 20, 27, 27, 27, 27, 43, 43, 74, 103, 201, 201, 201, 201, 201, 27, 1, 7, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 20, 20, 27, 27, 27, 27, 27, 74, 74, 201, 27, 27, 1, 1, 8, 8] 201 rigid atoms, others: [42, 43, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 538 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478517 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 118, 57, 57, 57, 57, 44, 36, 44, 13, 1, 1, 1, 1, 1, 1, 1, 57, 138, 164, 164, 201, 201, 201, 201, 201, 201, 138, 138, 138, 118, 118, 57, 57, 57, 57, 57, 36, 36, 1, 57, 57, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 774 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478517 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478517 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478517/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478517 Building REAL300025478518 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478518' /scratch/stefan/7787258/working/building/REAL300025478518 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478518 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478518/0 /scratch/stefan/7787258/working/building/REAL300025478518 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/402 `/scratch/stefan/7787258/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCCC[C@H]1O) `REAL300025478518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478518 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 66, 66, 66, 66, 66, 1, 10, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 15, 15, 66, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 69] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 269 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: REAL300025478518 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 8, 15, 23, 23, 23, 23, 37, 37, 76, 109, 201, 201, 201, 201, 201, 23, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 15, 23, 23, 23, 23, 23, 76, 76, 201, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 3] 603 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 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, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 52]) total number of confs: 520 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: REAL300025478518 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@@H]1CCCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [141, 130, 66, 66, 66, 66, 44, 36, 44, 12, 1, 1, 1, 1, 1, 1, 1, 66, 141, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 141, 141, 141, 130, 130, 66, 66, 66, 66, 66, 36, 36, 1, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 603] 603 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1353 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478518 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478518 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478518/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478518 Building REAL300025478519 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478519' /scratch/stefan/7787258/working/building/REAL300025478519 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478519 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478519/0 /scratch/stefan/7787258/working/building/REAL300025478519 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/403 `/scratch/stefan/7787258/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)C=CCCC1) `REAL300025478519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478519 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)C=CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 43, 113, 113, 113, 113, 113, 1, 10, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 22, 22, 113, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 264 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478519 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)C=CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 11, 16, 16, 16, 16, 30, 30, 60, 102, 201, 201, 201, 201, 201, 16, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 16, 16, 16, 16, 16, 60, 60, 201, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 495 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478519 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(C)C=CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 151, 113, 113, 113, 113, 63, 29, 63, 12, 1, 1, 1, 1, 1, 1, 1, 113, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 151, 151, 113, 113, 113, 113, 113, 29, 29, 1, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 623 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478519 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478519 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478519/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478519 Building REAL300025478520 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478520' /scratch/stefan/7787258/working/building/REAL300025478520 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478520 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478520/0 /scratch/stefan/7787258/working/building/REAL300025478520 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/404 `/scratch/stefan/7787258/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2(CC2)C1) `REAL300025478520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478520 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 14, 40, 40, 40, 40, 40, 1, 13, 19, 19, 20, 38, 38, 38, 38, 38, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 40, 1, 1, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478520 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 30, 38, 38, 38, 38, 51, 51, 99, 121, 201, 201, 201, 201, 201, 38, 5, 11, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 30, 30, 38, 38, 38, 38, 38, 99, 99, 201, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 583 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478520 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 81, 40, 40, 40, 40, 32, 28, 32, 11, 1, 1, 1, 1, 1, 1, 1, 40, 101, 118, 118, 127, 201, 201, 201, 201, 201, 101, 101, 101, 81, 81, 40, 40, 40, 40, 40, 28, 28, 1, 40, 40, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478520 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478520 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478520/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478520 Building REAL300025478521 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478521' /scratch/stefan/7787258/working/building/REAL300025478521 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478521 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478521/0 /scratch/stefan/7787258/working/building/REAL300025478521 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/405 `/scratch/stefan/7787258/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1C) `REAL300025478521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478521 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 14, 14, 29, 45, 45, 45, 45, 56, 56, 99, 123, 201, 201, 201, 201, 201, 45, 1, 1, 1, 2, 2, 2, 1, 14, 14, 14, 29, 29, 45, 45, 45, 45, 45, 99, 99, 201, 45, 45, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 596 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: REAL300025478521 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 112, 119, 99, 112, 56, 56, 56, 56, 49, 37, 49, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 112, 112, 112, 99, 99, 56, 56, 56, 56, 56, 37, 37, 1, 56, 56, 201, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 597 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: REAL300025478521 none CC1=CC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 18, 12, 18, 6, 12, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 56, 56, 56, 56, 56, 1, 45, 45, 45, 45, 45, 45, 45, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 9, 9, 56, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478521 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478521 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478521/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478521 Building REAL300025478522 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478522' /scratch/stefan/7787258/working/building/REAL300025478522 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478522 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478522/0 /scratch/stefan/7787258/working/building/REAL300025478522 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/406 `/scratch/stefan/7787258/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1) `REAL300025478522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478522 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 16, 19, 6, 16, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 79, 79, 79, 79, 79, 1, 26, 31, 31, 31, 31, 26, 26, 26, 26, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 16, 16, 79, 1, 1, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [11, 36, 37, 6, 7, 8, 9, 10, 39, 44, 45, 40, 21, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 262 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: REAL300025478522 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 5, 7, 7, 16, 31, 31, 31, 31, 47, 47, 88, 121, 201, 201, 201, 201, 201, 31, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 16, 16, 31, 31, 31, 31, 31, 88, 88, 201, 31, 31, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 536 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478522 none CC(C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 198, 199, 170, 198, 79, 79, 79, 79, 56, 42, 56, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 170, 170, 79, 79, 79, 79, 79, 42, 42, 1, 79, 79, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 777 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478522 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478522 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478522/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478522 Building REAL300025478523 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478523' /scratch/stefan/7787258/working/building/REAL300025478523 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478523 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478523/0 /scratch/stefan/7787258/working/building/REAL300025478523 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/407 `/scratch/stefan/7787258/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(Cl)=C1) `REAL300025478523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478523 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 16, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 56, 56, 56, 56, 56, 1, 12, 22, 22, 48, 48, 48, 48, 48, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 56, 1, 1, 48, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 206 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: REAL300025478523 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 16, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 20, 38, 48, 48, 48, 48, 64, 64, 109, 134, 201, 201, 201, 201, 201, 48, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 38, 38, 48, 48, 48, 48, 48, 109, 109, 201, 48, 48, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 603 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: REAL300025478523 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 1, 16, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 96, 56, 56, 56, 56, 49, 40, 49, 13, 1, 1, 1, 1, 1, 1, 1, 56, 107, 147, 147, 201, 201, 201, 201, 201, 107, 107, 107, 96, 96, 56, 56, 56, 56, 56, 40, 40, 1, 56, 56, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 659 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478523 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478523 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478523/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478523 Building REAL300025478524 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478524' /scratch/stefan/7787258/working/building/REAL300025478524 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478524 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478524/0 /scratch/stefan/7787258/working/building/REAL300025478524 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/408 `/scratch/stefan/7787258/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H]([NH+](C)C)C1) `REAL300025478524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478524 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H]([NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 9, 22, 22, 22, 22, 22, 1, 6, 9, 9, 11, 11, 11, 11, 11, 14, 14, 14, 11, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 7, 7, 22, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11] 32 rigid atoms, others: [2, 3, 4, 5, 6, 39, 7, 44, 17, 35, 43, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 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: REAL300025478524 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H]([NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 4, 5, 9, 11, 11, 11, 11, 13, 13, 23, 24, 32, 32, 32, 32, 32, 11, 1, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 9, 9, 11, 11, 11, 11, 11, 23, 23, 32, 11, 11, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 32 rigid atoms, others: [54, 45, 46, 18, 20, 21, 22, 23, 24, 25, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 135 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: REAL300025478524 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)[C@H]1C[C@H]([NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 7, 5, 5, 7, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 22, 22, 22, 22, 20, 19, 20, 12, 1, 1, 1, 1, 1, 1, 1, 22, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 26, 26, 22, 22, 22, 22, 22, 19, 19, 1, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478524 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478524 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478524/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478524 Building REAL300025478525 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478525' /scratch/stefan/7787258/working/building/REAL300025478525 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478525 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478525/0 /scratch/stefan/7787258/working/building/REAL300025478525 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/409 `/scratch/stefan/7787258/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478525 none CC(CC[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 8, 8, 11, 11, 11, 6, 7, 5, 6, 1, 1, 1, 1, 1, 1, 4, 4, 9, 10, 17, 17, 17, 17, 17, 1, 7, 7, 7, 7, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 9, 9, 17, 1, 1] 19 rigid atoms, others: [16, 17, 47, 12, 13, 14, 15, 48, 49, 50, 51, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478525 none CC(CC[NH+](C)C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 17, 10, 1, 1, 1, 1, 1, 1, 1, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17] 19 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 59 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478525 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478525 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478525/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478525 Building REAL300025478526 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478526' /scratch/stefan/7787258/working/building/REAL300025478526 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478526 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478526/0 /scratch/stefan/7787258/working/building/REAL300025478526 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/410 `/scratch/stefan/7787258/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C2CC2)C1) `REAL300025478526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025478526 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 20, 48, 48, 48, 48, 48, 1, 12, 24, 24, 32, 32, 32, 36, 36, 32, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 48, 1, 1, 32, 32, 32, 32, 36, 36, 36, 36, 36, 32, 32] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478526 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 27, 36, 36, 36, 36, 52, 52, 94, 120, 201, 201, 201, 201, 201, 36, 2, 8, 2, 2, 1, 1, 1, 1, 2, 14, 14, 14, 27, 27, 36, 36, 36, 36, 36, 94, 94, 201, 36, 36, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2] 201 rigid atoms, others: [46, 47, 48, 49, 50, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 51, 52]) total number of confs: 555 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478526 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 23, 32, 32, 32, 32, 49, 49, 90, 116, 201, 201, 201, 201, 201, 32, 1, 5, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 90, 90, 201, 32, 32, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 51, 20, 21, 22, 23, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 543 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478526 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC(C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 110, 48, 48, 48, 48, 36, 31, 36, 12, 1, 1, 1, 1, 1, 1, 1, 48, 134, 159, 159, 201, 201, 201, 201, 201, 201, 134, 134, 134, 110, 110, 48, 48, 48, 48, 48, 31, 31, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 759 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478526 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478526 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478526/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478526 Building REAL300025478527 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478527' /scratch/stefan/7787258/working/building/REAL300025478527 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478527 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478527/0 /scratch/stefan/7787258/working/building/REAL300025478527 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/411 `/scratch/stefan/7787258/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478527 none CC(C)[C@H](NC=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [20, 17, 20, 12, 17, 17, 23, 23, 10, 12, 5, 10, 1, 1, 1, 1, 1, 1, 4, 4, 10, 17, 65, 65, 65, 65, 65, 1, 20, 20, 20, 20, 20, 20, 20, 23, 23, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 65, 1, 1] 131 rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 50, 51, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49]) total number of confs: 212 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: REAL300025478527 none CC(C)[C@H](NC=O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 129, 131, 123, 129, 129, 130, 130, 122, 123, 107, 122, 65, 65, 65, 65, 53, 39, 53, 13, 1, 1, 1, 1, 1, 1, 1, 65, 131, 131, 131, 131, 131, 131, 131, 130, 130, 122, 122, 122, 107, 107, 65, 65, 65, 65, 65, 39, 39, 1, 65, 65] 131 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 511 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478527 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478527 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478527/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478527 Building REAL300025478528 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478528' /scratch/stefan/7787258/working/building/REAL300025478528 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478528 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478528/0 /scratch/stefan/7787258/working/building/REAL300025478528 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/412 `/scratch/stefan/7787258/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478528 none CCSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 5, 5, 11, 11, 24, 37, 37, 37, 37, 50, 50, 88, 111, 201, 201, 201, 201, 201, 37, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 24, 24, 37, 37, 37, 37, 37, 88, 88, 201, 37, 37, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 46, 47, 48, 49, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478528 none CCSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 133, 187, 108, 133, 54, 54, 54, 54, 41, 34, 41, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 108, 108, 54, 54, 54, 54, 54, 34, 34, 1, 54, 54, 201, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 755 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478528 none CCSC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 41, 37, 26, 11, 26, 5, 11, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 54, 54, 54, 54, 54, 1, 37, 37, 44, 44, 44, 44, 44, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 54, 1, 1, 37, 37, 37, 37] 201 rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 44, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478528 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478528 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478528/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478528 Building REAL300025478529 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478529' /scratch/stefan/7787258/working/building/REAL300025478529 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478529 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478529/0 /scratch/stefan/7787258/working/building/REAL300025478529 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/413 `/scratch/stefan/7787258/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478529 none CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 25, 50, 25, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 68, 68, 68, 68, 68, 1, 50, 50, 50, 50, 50, 50, 25, 25, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 68, 1, 1] 201 rigid atoms, others: [48, 43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 49, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47]) total number of confs: 265 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: REAL300025478529 none CN(C)C(=O)C=CC(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 201, 173, 152, 152, 152, 122, 152, 68, 68, 68, 68, 52, 41, 52, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 173, 173, 152, 152, 152, 122, 122, 68, 68, 68, 68, 68, 41, 41, 1, 68, 68] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 781 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478529 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478529 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478529/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478529 Building REAL300025478530 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478530' /scratch/stefan/7787258/working/building/REAL300025478530 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478530 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478530/0 /scratch/stefan/7787258/working/building/REAL300025478530 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/414 `/scratch/stefan/7787258/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478530 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 5, 5, 18, 34, 34, 34, 34, 46, 46, 74, 110, 201, 201, 201, 201, 201, 34, 1, 1, 1, 5, 5, 5, 18, 18, 34, 34, 34, 34, 34, 74, 74, 201, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478530 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 134, 144, 113, 134, 53, 53, 53, 53, 39, 27, 39, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 134, 134, 134, 113, 113, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53, 201, 201, 201, 201] 201 rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 798 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478530 none C#CC1(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 26, 6, 14, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 53, 53, 53, 53, 53, 1, 34, 34, 34, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 7, 7, 53, 1, 1, 34, 34, 34, 34] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478530 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478530 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478530/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478530 Building REAL300025478531 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478531' /scratch/stefan/7787258/working/building/REAL300025478531 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478531 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478531/0 /scratch/stefan/7787258/working/building/REAL300025478531 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/415 `/scratch/stefan/7787258/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1) `REAL300025478531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478531 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 12, 12, 24, 38, 38, 38, 38, 52, 52, 87, 117, 201, 201, 201, 201, 201, 38, 1, 1, 2, 2, 2, 12, 12, 12, 24, 24, 38, 38, 38, 38, 38, 87, 87, 201, 38, 38, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478531 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 131, 141, 111, 131, 54, 54, 54, 54, 38, 30, 38, 12, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 131, 131, 131, 111, 111, 54, 54, 54, 54, 54, 30, 30, 1, 54, 54, 201] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 667 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478531 none CC1=NC(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 17, 10, 17, 5, 10, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 54, 54, 54, 54, 54, 1, 38, 38, 38, 38, 38, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 9, 9, 54, 1, 1, 38] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478531 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478531 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478531/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478531 Building REAL300025478532 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478532' /scratch/stefan/7787258/working/building/REAL300025478532 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478532 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478532/0 /scratch/stefan/7787258/working/building/REAL300025478532 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/416 `/scratch/stefan/7787258/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COCC1) `REAL300025478532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478532 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 60, 60, 60, 60, 60, 1, 15, 35, 35, 46, 46, 46, 46, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 11, 11, 60, 1, 1, 46, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 229 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: REAL300025478532 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 28, 46, 46, 46, 46, 61, 61, 101, 121, 201, 201, 201, 201, 201, 46, 1, 7, 1, 1, 1, 1, 1, 12, 12, 12, 28, 28, 46, 46, 46, 46, 46, 101, 101, 201, 46, 46, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 585 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478532 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.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: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 12, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 129, 60, 60, 60, 60, 50, 42, 50, 13, 1, 1, 1, 1, 1, 1, 1, 60, 154, 176, 176, 201, 201, 201, 201, 154, 154, 154, 129, 129, 60, 60, 60, 60, 60, 42, 42, 1, 60, 60, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 742 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478532 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478532 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478532/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478532 Building REAL300025478533 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478533' /scratch/stefan/7787258/working/building/REAL300025478533 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478533 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478533/0 /scratch/stefan/7787258/working/building/REAL300025478533 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/417 `/scratch/stefan/7787258/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCSC1) `REAL300025478533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478533 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 61, 61, 61, 61, 61, 1, 12, 22, 22, 33, 33, 33, 33, 33, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 61, 1, 1, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 196 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: REAL300025478533 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 24, 33, 33, 33, 33, 48, 48, 86, 113, 201, 201, 201, 201, 201, 33, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 33, 33, 33, 33, 33, 86, 86, 201, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 548 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: REAL300025478533 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CCCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 5, 5, 14, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 121, 61, 61, 61, 61, 47, 38, 47, 12, 1, 1, 1, 1, 1, 1, 1, 61, 145, 178, 178, 201, 201, 201, 201, 201, 145, 145, 145, 121, 121, 61, 61, 61, 61, 61, 38, 38, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 735 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478533 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478533 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478533/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478533 Building REAL300025478534 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478534' /scratch/stefan/7787258/working/building/REAL300025478534 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478534 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478534/0 /scratch/stefan/7787258/working/building/REAL300025478534 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/418 `/scratch/stefan/7787258/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478534 none C[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 22, 33, 33, 13, 22, 5, 13, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 66, 66, 66, 66, 66, 1, 33, 33, 33, 99, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 66, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 327 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478534 none C[C@H](O)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [201, 194, 201, 201, 167, 194, 110, 167, 66, 66, 66, 66, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 603, 167, 167, 167, 110, 110, 66, 66, 66, 66, 66, 35, 35, 1, 66, 66] 603 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 1355 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478534 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478534 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478534/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478534 Building REAL300025478535 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478535' /scratch/stefan/7787258/working/building/REAL300025478535 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478535 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478535/0 /scratch/stefan/7787258/working/building/REAL300025478535 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/419 `/scratch/stefan/7787258/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(F)=NN1) `REAL300025478535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478535 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(F)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 15, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 15, 21, 62, 62, 62, 62, 62, 1, 13, 30, 30, 49, 49, 49, 49, 49, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 15, 15, 62, 1, 1, 49, 49] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42]) total number of confs: 244 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: REAL300025478535 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(F)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 15, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 20, 38, 49, 49, 49, 49, 72, 72, 112, 137, 201, 201, 201, 201, 201, 49, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 38, 38, 49, 49, 49, 49, 49, 112, 112, 201, 49, 49, 1, 1] 201 rigid atoms, others: [41, 42, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 603 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: REAL300025478535 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(F)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 15, 8, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 112, 62, 62, 62, 62, 52, 43, 52, 13, 1, 1, 1, 1, 1, 1, 1, 62, 129, 177, 177, 201, 201, 201, 201, 201, 129, 129, 129, 112, 112, 62, 62, 62, 62, 62, 43, 43, 1, 62, 62, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 706 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478535 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478535 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478535/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478535 Building REAL300025478536 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478536' /scratch/stefan/7787258/working/building/REAL300025478536 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478536 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478536/0 /scratch/stefan/7787258/working/building/REAL300025478536 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/420 `/scratch/stefan/7787258/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C=CCC1) `REAL300025478536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478536 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 69, 69, 69, 69, 69, 1, 13, 24, 24, 37, 37, 37, 37, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 69, 1, 1, 37, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 17, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 245 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: REAL300025478536 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 29, 37, 37, 37, 37, 45, 45, 86, 112, 201, 201, 201, 201, 201, 37, 1, 6, 1, 1, 1, 1, 1, 16, 16, 16, 29, 29, 37, 37, 37, 37, 37, 86, 86, 201, 37, 37, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 541 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: REAL300025478536 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 134, 69, 69, 69, 69, 50, 40, 50, 13, 1, 1, 1, 1, 1, 1, 1, 69, 147, 171, 171, 201, 201, 201, 201, 147, 147, 147, 134, 134, 69, 69, 69, 69, 69, 40, 40, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 806 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478536 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478536 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478536/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478536 Building REAL300025478537 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478537' /scratch/stefan/7787258/working/building/REAL300025478537 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478537 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478537/0 /scratch/stefan/7787258/working/building/REAL300025478537 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/421 `/scratch/stefan/7787258/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC(O)C1) `REAL300025478537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478537 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 69, 69, 69, 69, 69, 1, 13, 25, 25, 31, 31, 31, 31, 31, 31, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 69, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 93, 31, 31] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 318 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478537 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 13, 24, 31, 31, 31, 31, 43, 43, 82, 110, 201, 201, 201, 201, 201, 31, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 31, 31, 31, 31, 31, 82, 82, 201, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1] 603 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 50]) total number of confs: 535 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478537 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CCCC(O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [167, 131, 69, 69, 69, 69, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 69, 167, 189, 189, 201, 201, 201, 201, 201, 201, 167, 167, 167, 131, 131, 69, 69, 69, 69, 69, 42, 42, 1, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 1382 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478537 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478537 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478537/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478537 Building REAL300025478538 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478538' /scratch/stefan/7787258/working/building/REAL300025478538 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478538 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478538/0 /scratch/stefan/7787258/working/building/REAL300025478538 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/422 `/scratch/stefan/7787258/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478538 none CC1CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 19, 32, 32, 32, 32, 50, 50, 92, 121, 201, 201, 201, 201, 201, 32, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 9, 9, 19, 19, 32, 32, 32, 32, 32, 92, 92, 201, 32, 32, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 51, 52, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478538 none CC1CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 182, 201, 156, 182, 73, 73, 73, 73, 50, 41, 50, 12, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 156, 156, 73, 73, 73, 73, 73, 41, 41, 1, 73, 73, 201, 201, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 767 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478538 none CC1CC=C(C(=O)N(C)CC2CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 25, 15, 25, 6, 15, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 73, 73, 73, 73, 73, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 16, 16, 73, 1, 1, 32, 32, 32, 32] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478538 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478538 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478538/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478538 Building REAL300025478539 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478539' /scratch/stefan/7787258/working/building/REAL300025478539 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478539 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478539/0 /scratch/stefan/7787258/working/building/REAL300025478539 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/423 `/scratch/stefan/7787258/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478539 none CC(O)C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 31, 17, 24, 14, 17, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 80, 80, 80, 80, 80, 1, 31, 31, 31, 31, 93, 24, 24, 24, 24, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 15, 15, 80, 1, 1] 603 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 47, 48, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 363 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478539 none CC(O)C(C)C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 200, 201, 193, 200, 191, 193, 165, 191, 80, 80, 80, 80, 55, 44, 55, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 603, 200, 200, 200, 200, 191, 191, 191, 165, 165, 80, 80, 80, 80, 80, 44, 44, 1, 80, 80] 603 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1382 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478539 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478539 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478539/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478539 Building REAL300025478540 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478540' /scratch/stefan/7787258/working/building/REAL300025478540 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478540 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478540/0 /scratch/stefan/7787258/working/building/REAL300025478540 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/424 `/scratch/stefan/7787258/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCOC1) `REAL300025478540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478540 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 3, 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: [18, 6, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 73, 73, 73, 73, 73, 1, 18, 30, 30, 36, 36, 36, 36, 36, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 9, 9, 73, 1, 1, 108, 36, 36, 36, 36, 36, 36] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 206 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478540 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 3, 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: [10, 6, 10, 22, 36, 36, 36, 36, 44, 44, 84, 114, 201, 201, 201, 201, 201, 36, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 36, 36, 36, 36, 36, 84, 84, 201, 36, 36, 6, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [42, 43, 44, 45, 46, 47, 18, 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, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 565 number of broken/clashed sets: 206 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478540 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1(O)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 7, 3, 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: [173, 143, 73, 73, 73, 73, 56, 41, 56, 13, 1, 1, 1, 1, 1, 1, 1, 73, 173, 193, 193, 201, 201, 201, 201, 201, 173, 173, 173, 143, 143, 73, 73, 73, 73, 73, 41, 41, 1, 73, 73, 603, 201, 201, 201, 201, 201, 201] 603 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 1375 number of broken/clashed sets: 206 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478540 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478540 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478540/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478540 Building REAL300025478541 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478541' /scratch/stefan/7787258/working/building/REAL300025478541 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478541 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478541/0 /scratch/stefan/7787258/working/building/REAL300025478541 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/425 `/scratch/stefan/7787258/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N(C)[N-]1) `REAL300025478541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478541 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N(C)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 4, 4, 11, 19, 66, 66, 66, 66, 66, 1, 17, 36, 36, 43, 43, 43, 43, 43, 43, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 11, 11, 66, 1, 1, 43, 43, 43, 43] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478541 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N(C)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 32, 43, 43, 43, 43, 51, 51, 93, 116, 201, 201, 201, 201, 201, 43, 1, 7, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 32, 32, 43, 43, 43, 43, 43, 93, 93, 201, 43, 43, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 18, 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, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478541 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1=CC(=O)N(C)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 8, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 66, 66, 66, 66, 46, 37, 46, 13, 1, 1, 1, 1, 1, 1, 1, 66, 151, 194, 194, 201, 201, 201, 201, 201, 201, 151, 151, 151, 122, 122, 66, 66, 66, 66, 66, 37, 37, 1, 66, 66, 201, 201, 201, 201] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478541 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478541 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478541/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478541 Building REAL300025478542 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478542' /scratch/stefan/7787258/working/building/REAL300025478542 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478542 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478542/0 /scratch/stefan/7787258/working/building/REAL300025478542 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/426 `/scratch/stefan/7787258/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478542 none C=C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 10, 10, 23, 34, 34, 34, 34, 50, 50, 89, 118, 201, 201, 201, 201, 201, 34, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 34, 34, 34, 34, 34, 89, 89, 201, 34, 34] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478542 none C=C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 147, 149, 131, 147, 71, 71, 71, 71, 51, 37, 51, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 147, 147, 147, 131, 131, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 755 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478542 none C=C1CC1C(=O)N(C)CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 18, 13, 18, 6, 13, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 71, 71, 71, 71, 71, 1, 34, 34, 34, 34, 34, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 14, 14, 71, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478542 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478542 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478542/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478542 Building REAL300025478543 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478543' /scratch/stefan/7787258/working/building/REAL300025478543 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478543 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478543/0 /scratch/stefan/7787258/working/building/REAL300025478543 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/427 `/scratch/stefan/7787258/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC=CC1) `REAL300025478543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478543 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 15, 39, 39, 39, 39, 39, 1, 12, 19, 19, 22, 36, 36, 36, 36, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 39, 1, 1, 22, 22, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 17, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478543 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 13, 27, 36, 36, 36, 36, 50, 50, 97, 122, 201, 201, 201, 201, 201, 36, 5, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 36, 36, 36, 36, 36, 97, 97, 201, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478543 none CN(CC1CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)CC1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 77, 39, 39, 39, 39, 32, 29, 32, 11, 1, 1, 1, 1, 1, 1, 1, 39, 95, 114, 114, 121, 201, 201, 201, 201, 95, 95, 95, 77, 77, 39, 39, 39, 39, 39, 29, 29, 1, 39, 39, 121, 121, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 804 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478543 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478543 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478543/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478543 Building REAL300025478544 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478544' /scratch/stefan/7787258/working/building/REAL300025478544 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478544 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478544/0 /scratch/stefan/7787258/working/building/REAL300025478544 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/428 `/scratch/stefan/7787258/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478544 none CN(CC1CCN(C(=O)CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 15, 21, 21, 1, 8, 12, 12, 18, 19, 46, 46, 46, 46, 46, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 15, 15, 21, 21, 21, 21, 21, 1, 1, 18, 18, 46] 109 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478544 none CN(CC1CCN(C(=O)CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [38, 36, 38, 41, 46, 46, 46, 46, 55, 55, 102, 109, 109, 46, 30, 36, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 41, 41, 46, 46, 46, 46, 46, 102, 102, 109, 109, 109, 109, 109, 46, 46, 30, 30, 1] 109 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 461 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478544 none CN(CC1CCN(C(=O)CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [57, 38, 21, 21, 21, 21, 11, 3, 11, 1, 1, 1, 1, 21, 57, 78, 78, 87, 87, 109, 109, 109, 109, 109, 57, 57, 57, 38, 38, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 21, 21, 87, 87, 109] 109 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478544 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478544 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478544/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478544 Building REAL300025478545 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478545' /scratch/stefan/7787258/working/building/REAL300025478545 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478545 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478545/0 /scratch/stefan/7787258/working/building/REAL300025478545 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/429 `/scratch/stefan/7787258/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(C)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478545 none CN(CC1CCN(C(=O)C(C)(C)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 15, 35, 35, 65, 88, 152, 152, 152, 152, 152, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 65, 65, 152] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 408 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478545 none CN(CC1CCN(C(=O)C(C)(C)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 59, 84, 132, 152, 152, 152, 152, 201, 201, 201, 201, 201, 152, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 132, 132, 152, 152, 152, 152, 152, 201, 201, 201, 201, 201, 201, 152, 152, 31, 31, 1] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 827 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478545 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478545 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478545/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478545 Building REAL300025478546 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478546' /scratch/stefan/7787258/working/building/REAL300025478546 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478546 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478546/0 /scratch/stefan/7787258/working/building/REAL300025478546 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/430 `/scratch/stefan/7787258/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478546 none CN(CC1CCN(C(=O)C(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 1, 11, 27, 27, 54, 74, 129, 129, 129, 129, 129, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 54, 54, 129] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 13, 37, 38, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41]) total number of confs: 363 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478546 none CN(CC1CCN(C(=O)C(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 63, 79, 115, 129, 129, 129, 129, 197, 197, 201, 201, 201, 129, 34, 63, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 115, 115, 129, 129, 129, 129, 129, 201, 201, 201, 129, 129, 34, 34, 1] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 827 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478546 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478546 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478546/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478546 Building REAL300025478547 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478547' /scratch/stefan/7787258/working/building/REAL300025478547 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478547 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478547/0 /scratch/stefan/7787258/working/building/REAL300025478547 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/431 `/scratch/stefan/7787258/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478547 none COCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 30, 46, 116, 116, 116, 116, 116, 1, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 116, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 42, 22, 41, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 299 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478547 none COCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 116, 157, 116, 116, 116, 97, 69, 49, 69, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 97, 97, 69, 69, 69, 27, 27, 1, 116, 116] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 871 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478547 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478547 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478547/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478547 Building REAL300025478548 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478548' /scratch/stefan/7787258/working/building/REAL300025478548 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478548 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478548/0 /scratch/stefan/7787258/working/building/REAL300025478548 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/432 `/scratch/stefan/7787258/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478548 none CN(CC1CCN(C(=O)C2=CC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 7, 7, 7, 1, 13, 32, 32, 57, 81, 154, 154, 154, 154, 154, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 7, 7, 1, 1, 57, 57, 154] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 389 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: REAL300025478548 none CN(CC1CCN(C(=O)C2=CC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 67, 87, 140, 154, 154, 154, 154, 199, 199, 201, 201, 201, 201, 201, 154, 33, 67, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 140, 140, 154, 154, 154, 154, 154, 201, 201, 201, 201, 154, 154, 33, 33, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 799 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: REAL300025478548 none CN(CC1CCN(C(=O)C2=CC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 6, 6, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 33, 64, 64, 107, 142, 201, 201, 201, 201, 201, 33, 33, 33, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 597 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478548 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478548 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478548/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478548 Building REAL300025478549 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478549' /scratch/stefan/7787258/working/building/REAL300025478549 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478549 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478549/0 /scratch/stefan/7787258/working/building/REAL300025478549 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/433 `/scratch/stefan/7787258/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478549 none CN(CC1CCN(C(=O)C2=CC=NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 1, 13, 33, 33, 67, 96, 179, 179, 179, 179, 179, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 67, 67, 179] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478549 none CN(CC1CCN(C(=O)C2=CC=NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 86, 109, 159, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 179, 41, 86, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 159, 159, 179, 179, 179, 179, 179, 201, 201, 201, 201, 179, 179, 41, 41, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 793 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478549 none CN(CC1CCN(C(=O)C2=CC=NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 35, 65, 65, 107, 139, 201, 201, 201, 201, 201, 35, 35, 35, 18, 18, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 107, 107, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 585 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478549 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478549 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478549/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478549 Building REAL300025478550 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478550' /scratch/stefan/7787258/working/building/REAL300025478550 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478550 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478550/0 /scratch/stefan/7787258/working/building/REAL300025478550 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/434 `/scratch/stefan/7787258/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(F)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478550 none CN(CC1CCN(C(=O)C2=CC=C(F)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 14, 36, 36, 73, 104, 179, 179, 179, 179, 179, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 73, 73, 179] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 482 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478550 none CN(CC1CCN(C(=O)C2=CC=C(F)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 82, 107, 158, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 179, 39, 82, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 158, 158, 179, 179, 179, 179, 179, 201, 201, 201, 201, 179, 179, 39, 39, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 793 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: REAL300025478550 none CN(CC1CCN(C(=O)C2=CC=C(F)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 18, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 37, 63, 63, 107, 139, 201, 201, 201, 201, 201, 37, 37, 37, 18, 18, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 107, 107, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 589 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478550 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478550 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478550/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478550 Building REAL300025478551 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478551' /scratch/stefan/7787258/working/building/REAL300025478551 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478551 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478551/0 /scratch/stefan/7787258/working/building/REAL300025478551 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/435 `/scratch/stefan/7787258/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478551 none CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 32, 50, 134, 134, 134, 134, 134, 1, 11, 11, 11, 10, 10, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 134, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 326 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478551 none CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 147, 134, 147, 134, 134, 134, 121, 86, 60, 86, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 121, 121, 86, 86, 86, 31, 31, 1, 134, 134] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 882 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478551 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478551 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478551/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478551 Building REAL300025478552 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478552' /scratch/stefan/7787258/working/building/REAL300025478552 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478552 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478552/0 /scratch/stefan/7787258/working/building/REAL300025478552 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/436 `/scratch/stefan/7787258/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478552 none CN(CC1CCN(C(=O)C2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 1, 14, 31, 31, 62, 93, 155, 155, 155, 155, 155, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 62, 62, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 410 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: REAL300025478552 none CN(CC1CCN(C(=O)C2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 89, 106, 142, 155, 155, 155, 155, 167, 167, 201, 201, 201, 201, 201, 155, 40, 89, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 142, 142, 155, 155, 155, 155, 155, 201, 201, 201, 201, 155, 155, 40, 40, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 713 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: REAL300025478552 none CN(CC1CCN(C(=O)C2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 40, 69, 69, 107, 146, 201, 201, 201, 201, 201, 40, 40, 40, 24, 24, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 107, 107, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 586 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478552 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478552 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478552/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478552 Building REAL300025478553 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478553' /scratch/stefan/7787258/working/building/REAL300025478553 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478553 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478553/0 /scratch/stefan/7787258/working/building/REAL300025478553 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/437 `/scratch/stefan/7787258/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478553 none CN(CC1CCN(C(=O)CC2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 17, 37, 37, 37, 37, 1, 9, 13, 13, 20, 21, 53, 53, 53, 53, 53, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 17, 17, 37, 37, 37, 1, 1, 20, 20, 53] 139 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 213 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: REAL300025478553 none CN(CC1CCN(C(=O)CC2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 44, 45, 48, 53, 53, 53, 53, 68, 68, 113, 139, 139, 139, 139, 53, 32, 44, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 48, 48, 53, 53, 53, 53, 53, 113, 113, 139, 139, 139, 53, 53, 32, 32, 1] 139 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: 502 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: REAL300025478553 none CN(CC1CCN(C(=O)CC2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [78, 58, 37, 37, 37, 37, 18, 4, 19, 1, 1, 1, 1, 1, 1, 37, 78, 95, 95, 112, 112, 139, 139, 139, 139, 139, 78, 78, 78, 58, 58, 37, 37, 37, 37, 37, 4, 4, 1, 1, 1, 37, 37, 112, 112, 139] 139 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 468 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478553 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478553 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478553/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478553 Building REAL300025478554 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478554' /scratch/stefan/7787258/working/building/REAL300025478554 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478554 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478554/0 /scratch/stefan/7787258/working/building/REAL300025478554 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/438 `/scratch/stefan/7787258/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478554 none CN(CC1CCN(C(=O)C2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 4, 1, 12, 30, 30, 51, 79, 153, 153, 153, 153, 153, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 51, 51, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 374 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: REAL300025478554 none CN(CC1CCN(C(=O)C2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 75, 84, 132, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 153, 37, 75, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 132, 132, 153, 153, 153, 153, 153, 201, 201, 201, 153, 153, 37, 37, 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: 805 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: REAL300025478554 none CN(CC1CCN(C(=O)C2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 5, 5, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 5, 20, 51, 51, 86, 129, 201, 201, 201, 201, 201, 20, 20, 20, 12, 12, 5, 5, 5, 4, 4, 1, 1, 1, 5, 5, 86, 86, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 527 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478554 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478554 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478554/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478554 Building REAL300025478555 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478555' /scratch/stefan/7787258/working/building/REAL300025478555 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478555 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478555/0 /scratch/stefan/7787258/working/building/REAL300025478555 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/439 `/scratch/stefan/7787258/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478555 none CC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 14, 14, 32, 49, 130, 130, 130, 130, 130, 1, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 32, 32, 130, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 319 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478555 none CC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 130, 188, 130, 130, 130, 110, 72, 49, 72, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 130, 110, 110, 72, 72, 72, 29, 29, 1, 130, 130] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 826 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478555 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478555 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478555/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478555 Building REAL300025478556 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478556' /scratch/stefan/7787258/working/building/REAL300025478556 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478556 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478556/0 /scratch/stefan/7787258/working/building/REAL300025478556 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/440 `/scratch/stefan/7787258/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1) `REAL300025478556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478556 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 26, 40, 40, 57, 57, 82, 124, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 26, 26, 40, 40, 40, 82, 82, 201, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 567 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: REAL300025478556 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 134, 159, 134, 134, 134, 107, 76, 58, 76, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 107, 107, 76, 76, 76, 28, 28, 1, 134, 134, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 679 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: REAL300025478556 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 23, 23, 41, 66, 134, 134, 134, 134, 134, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 41, 41, 134, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 330 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478556 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478556 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478556/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478556 Building REAL300025478557 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478557' /scratch/stefan/7787258/working/building/REAL300025478557 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478557 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478557/0 /scratch/stefan/7787258/working/building/REAL300025478557 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/441 `/scratch/stefan/7787258/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1) `REAL300025478557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478557 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 30, 40, 40, 49, 49, 75, 115, 201, 201, 201, 201, 201, 11, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 30, 30, 40, 40, 40, 75, 75, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 545 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478557 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 157, 137, 157, 137, 137, 137, 113, 83, 56, 83, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 113, 113, 83, 83, 83, 28, 28, 1, 137, 137] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 687 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478557 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 6, 11, 11, 20, 20, 38, 62, 137, 137, 137, 137, 137, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 38, 38, 137, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 330 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478557 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478557 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478557/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478557 Building REAL300025478558 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478558' /scratch/stefan/7787258/working/building/REAL300025478558 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478558 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478558/0 /scratch/stefan/7787258/working/building/REAL300025478558 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/442 `/scratch/stefan/7787258/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C=CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478558 none CN(CC1CCN(C(=O)C=CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 4, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 19, 19, 19, 18, 1, 6, 9, 9, 12, 12, 21, 21, 21, 21, 21, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 12, 12, 19, 19, 19, 1, 1, 12, 12, 21] 37 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 104 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: REAL300025478558 none CN(CC1CCN(C(=O)C=CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 20, 21, 21, 21, 21, 25, 25, 34, 34, 37, 37, 37, 37, 21, 17, 18, 11, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 20, 20, 21, 21, 21, 21, 21, 34, 34, 37, 37, 37, 21, 21, 17, 17, 1] 37 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 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: REAL300025478558 none CN(CC1CCN(C(=O)C=CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 22, 19, 19, 19, 19, 15, 5, 14, 5, 1, 1, 1, 1, 1, 1, 19, 24, 26, 26, 29, 29, 37, 37, 37, 37, 37, 24, 24, 24, 22, 22, 19, 19, 19, 19, 19, 6, 5, 1, 1, 1, 19, 19, 29, 29, 37] 37 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478558 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478558 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478558/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478558 Building REAL300025478559 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478559' /scratch/stefan/7787258/working/building/REAL300025478559 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478559 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478559/0 /scratch/stefan/7787258/working/building/REAL300025478559 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/443 `/scratch/stefan/7787258/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478559 none CN(CC1CCN(C(=O)C2=CC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 6, 12, 12, 12, 1, 14, 34, 34, 60, 81, 145, 145, 145, 145, 145, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 60, 60, 145] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 424 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478559 none CN(CC1CCN(C(=O)C2=CC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 64, 79, 124, 145, 145, 145, 145, 151, 151, 201, 201, 199, 201, 201, 201, 145, 33, 64, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 124, 124, 145, 145, 145, 145, 145, 201, 201, 201, 201, 145, 145, 33, 33, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 726 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478559 none CN(CC1CCN(C(=O)C2=CC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 26, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 46, 78, 78, 115, 143, 201, 201, 201, 201, 201, 46, 46, 46, 26, 26, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 115, 115, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 610 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478559 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478559 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478559/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478559 Building REAL300025478560 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478560' /scratch/stefan/7787258/working/building/REAL300025478560 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478560 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478560/0 /scratch/stefan/7787258/working/building/REAL300025478560 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/444 `/scratch/stefan/7787258/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478560 none CN(CC1CCN(C(=O)C2=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 5, 6, 6, 1, 12, 33, 33, 70, 99, 179, 179, 179, 179, 179, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 5, 6, 6, 1, 1, 70, 70, 179] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 475 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478560 none CN(CC1CCN(C(=O)C2=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 81, 110, 160, 179, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 179, 39, 81, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 160, 160, 179, 179, 179, 179, 179, 201, 201, 201, 201, 201, 179, 179, 39, 39, 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: 800 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: REAL300025478560 none CN(CC1CCN(C(=O)C2=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 30, 54, 54, 100, 131, 201, 201, 201, 201, 201, 30, 30, 30, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 100, 100, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 589 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478560 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478560 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478560/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478560 Building REAL300025478561 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478561' /scratch/stefan/7787258/working/building/REAL300025478561 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478561 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478561/0 /scratch/stefan/7787258/working/building/REAL300025478561 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/445 `/scratch/stefan/7787258/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478561 none CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 19, 19, 36, 60, 122, 122, 122, 122, 122, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 36, 36, 122, 1, 1] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 317 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478561 none CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 122, 132, 122, 122, 122, 114, 77, 52, 77, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 114, 114, 77, 77, 77, 28, 28, 1, 122, 122] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 924 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478561 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478561 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478561/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478561 Building REAL300025478562 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478562' /scratch/stefan/7787258/working/building/REAL300025478562 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478562 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478562/0 /scratch/stefan/7787258/working/building/REAL300025478562 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/446 `/scratch/stefan/7787258/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478562 none CN(CC1CCN(C(=O)C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 12, 30, 30, 58, 76, 126, 126, 126, 126, 126, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 58, 58, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 366 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478562 none CN(CC1CCN(C(=O)C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 61, 77, 111, 126, 126, 126, 126, 133, 133, 201, 201, 201, 201, 201, 126, 35, 61, 13, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 111, 111, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 35, 35, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 810 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478562 none CN(CC1CCN(C(=O)C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 29, 58, 58, 107, 136, 201, 201, 201, 201, 201, 29, 29, 29, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [45, 43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 47, 48, 49, 50, 51]) total number of confs: 607 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478562 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478562 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478562/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478562 Building REAL300025478563 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478563' /scratch/stefan/7787258/working/building/REAL300025478563 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478563 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478563/0 /scratch/stefan/7787258/working/building/REAL300025478563 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/447 `/scratch/stefan/7787258/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478563 none CN(CC1CCN(C(=O)C2=CN=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 1, 13, 31, 31, 64, 91, 168, 168, 168, 168, 168, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 64, 64, 168] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 433 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478563 none CN(CC1CCN(C(=O)C2=CN=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 79, 95, 148, 168, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201, 168, 37, 79, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 148, 148, 168, 168, 168, 168, 168, 201, 201, 201, 168, 168, 37, 37, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 797 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478563 none CN(CC1CCN(C(=O)C2=CN=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 29, 59, 59, 109, 140, 201, 201, 201, 201, 201, 29, 29, 29, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 109, 109, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 601 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478563 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478563 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478563/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478563 Building REAL300025478564 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478564' /scratch/stefan/7787258/working/building/REAL300025478564 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478564 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478564/0 /scratch/stefan/7787258/working/building/REAL300025478564 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/448 `/scratch/stefan/7787258/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478564 none CC1=CC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 21, 34, 34, 51, 51, 84, 128, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 34, 34, 34, 84, 84, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 574 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478564 none CC1=CC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 130, 117, 130, 117, 117, 117, 100, 78, 59, 78, 26, 59, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 130, 201, 201, 117, 117, 117, 117, 117, 100, 100, 78, 78, 78, 26, 26, 1, 117, 117] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 687 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478564 none CC1=CC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 33, 52, 117, 117, 117, 117, 117, 1, 8, 8, 8, 8, 3, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 33, 33, 117, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 295 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478564 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478564 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478564/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478564 Building REAL300025478565 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478565' /scratch/stefan/7787258/working/building/REAL300025478565 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478565 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478565/0 /scratch/stefan/7787258/working/building/REAL300025478565 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/449 `/scratch/stefan/7787258/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478565 none CN(CC1CCN(C(=O)CC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 20, 34, 34, 34, 34, 1, 8, 12, 12, 16, 16, 41, 41, 41, 41, 41, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 16, 16, 41] 134 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478565 none CN(CC1CCN(C(=O)CC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [35, 33, 35, 37, 41, 41, 41, 41, 52, 52, 125, 134, 134, 134, 134, 41, 29, 33, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 37, 37, 41, 41, 41, 41, 41, 125, 125, 134, 134, 134, 134, 134, 134, 134, 134, 134, 41, 41, 29, 29, 1] 134 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 545 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478565 none CN(CC1CCN(C(=O)CC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [75, 53, 34, 34, 34, 34, 17, 6, 17, 1, 1, 1, 1, 1, 1, 34, 75, 94, 94, 101, 101, 134, 134, 134, 134, 134, 75, 75, 75, 53, 53, 34, 34, 34, 34, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 101, 101, 134] 134 rigid atoms, others: [45, 43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 42] 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, 47, 48, 49, 50, 51]) total number of confs: 428 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478565 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478565 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478565/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478565 Building REAL300025478566 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478566' /scratch/stefan/7787258/working/building/REAL300025478566 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478566 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478566/0 /scratch/stefan/7787258/working/building/REAL300025478566 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/450 `/scratch/stefan/7787258/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478566 none CN(CC1CCN(C(=O)CCC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 22, 35, 35, 35, 35, 1, 8, 12, 12, 17, 17, 41, 41, 41, 41, 41, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 16, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 17, 17, 41] 146 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 239 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478566 none CN(CC1CCN(C(=O)CCC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [35, 33, 35, 37, 41, 41, 41, 41, 52, 52, 103, 109, 146, 146, 146, 146, 41, 28, 33, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 37, 37, 41, 41, 41, 41, 41, 103, 103, 111, 111, 146, 146, 146, 146, 146, 146, 146, 146, 146, 41, 41, 28, 28, 1] 146 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 620 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478566 none CN(CC1CCN(C(=O)CCC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [80, 56, 35, 35, 35, 35, 22, 8, 22, 5, 1, 1, 1, 1, 1, 1, 35, 80, 99, 99, 111, 111, 146, 146, 146, 146, 146, 80, 80, 80, 56, 56, 35, 35, 35, 35, 35, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 111, 111, 146] 146 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 498 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478566 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478566 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478566/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478566 Building REAL300025478567 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478567' /scratch/stefan/7787258/working/building/REAL300025478567 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478567 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478567/0 /scratch/stefan/7787258/working/building/REAL300025478567 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/451 `/scratch/stefan/7787258/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478567 none CN(CC1CCN(C(=O)C2=CC=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 1, 13, 30, 30, 56, 79, 137, 137, 137, 137, 137, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 56, 56, 137] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 372 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478567 none CN(CC1CCN(C(=O)C2=CC=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 71, 85, 121, 137, 137, 137, 137, 143, 143, 201, 201, 201, 201, 201, 201, 137, 37, 71, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 121, 121, 137, 137, 137, 137, 137, 201, 201, 201, 201, 137, 137, 37, 37, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478567 none CN(CC1CCN(C(=O)C2=CC=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 25, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 46, 75, 75, 111, 142, 201, 201, 201, 201, 201, 46, 46, 46, 25, 25, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 111, 111, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 616 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478567 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478567 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478567/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478567 Building REAL300025478568 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478568' /scratch/stefan/7787258/working/building/REAL300025478568 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478568 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478568/0 /scratch/stefan/7787258/working/building/REAL300025478568 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/452 `/scratch/stefan/7787258/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478568 none CN(CC1CCN(C(=O)C2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 1, 13, 29, 29, 51, 71, 126, 126, 126, 126, 126, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 51, 51, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478568 none CN(CC1CCN(C(=O)C2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 65, 69, 106, 126, 126, 126, 126, 145, 145, 201, 201, 201, 201, 126, 39, 65, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 106, 106, 126, 126, 126, 126, 126, 201, 201, 201, 126, 126, 39, 39, 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: 698 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478568 none CN(CC1CCN(C(=O)C2=CC=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 23, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 10, 35, 65, 65, 105, 139, 201, 201, 201, 201, 201, 35, 35, 35, 23, 23, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 105, 105, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 599 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478568 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478568 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478568/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478568 Building REAL300025478569 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478569' /scratch/stefan/7787258/working/building/REAL300025478569 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478569 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478569/0 /scratch/stefan/7787258/working/building/REAL300025478569 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/453 `/scratch/stefan/7787258/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1) `REAL300025478569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478569 none CC1=CN=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 21, 30, 30, 49, 49, 75, 118, 201, 201, 201, 201, 201, 8, 1, 1, 2, 2, 2, 1, 8, 8, 8, 8, 8, 21, 21, 30, 30, 30, 75, 75, 201, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 25, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 530 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478569 none CC1=CN=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 201, 168, 168, 168, 149, 101, 67, 101, 26, 67, 13, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 149, 149, 101, 101, 101, 26, 26, 1, 168, 168, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 738 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478569 none CC1=CN=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 6, 12, 12, 26, 26, 48, 81, 168, 168, 168, 168, 168, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 48, 48, 168, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 407 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478569 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478569 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478569/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478569 Building REAL300025478570 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478570' /scratch/stefan/7787258/working/building/REAL300025478570 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478570 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478570/0 /scratch/stefan/7787258/working/building/REAL300025478570 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/454 `/scratch/stefan/7787258/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478570 none CN(CC1CCN(C(=O)CC2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 16, 31, 31, 31, 31, 1, 9, 12, 12, 19, 19, 41, 41, 41, 41, 41, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 17, 17, 32, 31, 32, 1, 1, 19, 19, 41] 149 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 194 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: REAL300025478570 none CN(CC1CCN(C(=O)CC2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 35, 41, 41, 41, 41, 50, 50, 85, 149, 149, 149, 149, 41, 27, 34, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 35, 35, 41, 41, 41, 41, 41, 85, 85, 149, 149, 149, 41, 41, 27, 27, 1] 149 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: 468 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: REAL300025478570 none CN(CC1CCN(C(=O)CC2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 56, 31, 31, 31, 31, 16, 4, 16, 1, 1, 1, 1, 1, 1, 31, 79, 93, 93, 117, 117, 149, 149, 149, 149, 149, 79, 79, 79, 56, 56, 31, 31, 31, 32, 32, 4, 4, 1, 1, 1, 31, 31, 117, 117, 149] 149 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 542 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478570 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478570 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478570/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478570 Building REAL300025478571 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478571' /scratch/stefan/7787258/working/building/REAL300025478571 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478571 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478571/0 /scratch/stefan/7787258/working/building/REAL300025478571 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/455 `/scratch/stefan/7787258/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478571 none CC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 15, 23, 23, 43, 43, 74, 121, 201, 201, 201, 201, 201, 6, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 23, 23, 23, 74, 74, 201, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 27, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 526 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478571 none CC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 173, 197, 173, 173, 173, 164, 112, 66, 112, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 173, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 173, 164, 164, 112, 112, 112, 28, 28, 1, 173, 173] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 758 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478571 none CC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 11, 11, 27, 27, 57, 94, 173, 173, 173, 173, 173, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 57, 57, 173, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 440 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478571 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478571 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478571/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478571 Building REAL300025478572 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478572' /scratch/stefan/7787258/working/building/REAL300025478572 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478572 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478572/0 /scratch/stefan/7787258/working/building/REAL300025478572 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/456 `/scratch/stefan/7787258/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478572 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 27, 39, 39, 47, 47, 72, 112, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 1, 1, 1, 12, 12, 12, 12, 12, 27, 27, 39, 39, 39, 72, 72, 201, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 530 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478572 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 201, 201, 122, 113, 122, 113, 113, 113, 92, 76, 53, 76, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 195, 201, 201, 113, 113, 113, 113, 113, 92, 92, 76, 76, 76, 29, 29, 1, 113, 113, 201] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 629 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478572 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 15, 15, 30, 46, 113, 113, 113, 113, 113, 1, 12, 12, 12, 12, 5, 12, 12, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 30, 30, 113, 1, 1, 12] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 282 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478572 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478572 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478572/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478572 Building REAL300025478573 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478573' /scratch/stefan/7787258/working/building/REAL300025478573 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478573 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478573/0 /scratch/stefan/7787258/working/building/REAL300025478573 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/457 `/scratch/stefan/7787258/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478573 none CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 27, 42, 107, 107, 107, 107, 107, 1, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 27, 27, 107, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 280 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478573 none CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 146, 107, 146, 107, 107, 107, 91, 65, 52, 65, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 193, 193, 107, 107, 107, 107, 107, 91, 91, 65, 65, 65, 29, 29, 1, 107, 107] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 862 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478573 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478573 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478573/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478573 Building REAL300025478574 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478574' /scratch/stefan/7787258/working/building/REAL300025478574 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478574 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478574/0 /scratch/stefan/7787258/working/building/REAL300025478574 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/458 `/scratch/stefan/7787258/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478574 none CC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 39, 61, 135, 135, 135, 135, 135, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 39, 39, 135, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 330 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478574 none CC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 135, 149, 135, 135, 135, 116, 83, 60, 83, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 116, 116, 83, 83, 83, 29, 29, 1, 135, 135] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 779 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478574 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478574 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478574/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478574 Building REAL300025478575 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478575' /scratch/stefan/7787258/working/building/REAL300025478575 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478575 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478575/0 /scratch/stefan/7787258/working/building/REAL300025478575 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/459 `/scratch/stefan/7787258/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478575 none CN(CC1CCN(C(=O)C2=COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 1, 12, 29, 29, 62, 90, 169, 169, 169, 169, 169, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 62, 62, 169] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 440 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478575 none CN(CC1CCN(C(=O)C2=COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 84, 101, 149, 169, 169, 169, 169, 185, 185, 201, 201, 201, 201, 201, 169, 39, 84, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 149, 149, 169, 169, 169, 169, 169, 201, 201, 201, 201, 201, 169, 169, 39, 39, 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: 757 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478575 none CN(CC1CCN(C(=O)C2=COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 26, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 35, 59, 59, 101, 133, 201, 201, 201, 201, 201, 35, 35, 35, 26, 26, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 101, 101, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 578 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478575 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478575 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478575/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478575 Building REAL300025478576 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478576' /scratch/stefan/7787258/working/building/REAL300025478576 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478576 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478576/0 /scratch/stefan/7787258/working/building/REAL300025478576 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/460 `/scratch/stefan/7787258/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=[N+]([O-])C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478576 none CN(CC1CCN(C(=O)C2=CC=[N+]([O-])C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 4, 4, 8, 8, 1, 16, 36, 36, 73, 104, 178, 178, 178, 178, 178, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 73, 73, 178] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 484 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478576 none CN(CC1CCN(C(=O)C2=CC=[N+]([O-])C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 80, 99, 153, 178, 178, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 40, 80, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 153, 153, 178, 178, 178, 178, 178, 201, 201, 201, 201, 178, 178, 40, 40, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 798 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478576 none CN(CC1CCN(C(=O)C2=CC=[N+]([O-])C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 41, 74, 74, 114, 146, 201, 201, 201, 201, 201, 41, 41, 41, 21, 21, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 114, 114, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 591 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478576 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478576 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478576/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478576 Building REAL300025478577 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478577' /scratch/stefan/7787258/working/building/REAL300025478577 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478577 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478577/0 /scratch/stefan/7787258/working/building/REAL300025478577 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/461 `/scratch/stefan/7787258/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC3C=CC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478577 none CN(CC1CCN(C(=O)C2CC3C=CC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 1, 12, 30, 30, 61, 82, 150, 150, 150, 150, 150, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 61, 61, 150] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 403 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478577 none CN(CC1CCN(C(=O)C2CC3C=CC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 71, 86, 128, 150, 150, 150, 150, 167, 167, 201, 201, 201, 201, 201, 201, 150, 36, 71, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 128, 128, 150, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 36, 36, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 809 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478577 none CN(CC1CCN(C(=O)C2CC3C=CC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 30, 64, 64, 109, 138, 201, 201, 201, 201, 201, 30, 30, 30, 18, 18, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 109, 109, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 599 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478577 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478577 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478577/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478577 Building REAL300025478578 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478578' /scratch/stefan/7787258/working/building/REAL300025478578 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478578 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478578/0 /scratch/stefan/7787258/working/building/REAL300025478578 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/462 `/scratch/stefan/7787258/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478578 none CC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 40, 66, 149, 149, 149, 149, 149, 1, 10, 10, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 40, 40, 149, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 379 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478578 none CC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 201, 149, 183, 149, 149, 149, 140, 95, 62, 95, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 140, 140, 95, 95, 95, 29, 29, 1, 149, 149] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 801 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478578 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478578 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478578/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478578 Building REAL300025478579 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478579' /scratch/stefan/7787258/working/building/REAL300025478579 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478579 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478579/0 /scratch/stefan/7787258/working/building/REAL300025478579 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/463 `/scratch/stefan/7787258/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478579 none CN(CC1CCN(C(=O)C2=NNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 1, 15, 29, 29, 54, 77, 140, 140, 140, 140, 140, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 54, 54, 140] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 377 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478579 none CN(CC1CCN(C(=O)C2=NNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 120, 140, 140, 140, 140, 177, 177, 201, 201, 201, 201, 201, 201, 140, 39, 79, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 120, 120, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140, 39, 39, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 744 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478579 none CN(CC1CCN(C(=O)C2=NNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 44, 65, 65, 110, 138, 201, 201, 201, 201, 201, 44, 44, 44, 22, 22, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 110, 110, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 619 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478579 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478579 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478579/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478579 Building REAL300025478580 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478580' /scratch/stefan/7787258/working/building/REAL300025478580 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478580 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478580/0 /scratch/stefan/7787258/working/building/REAL300025478580 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/464 `/scratch/stefan/7787258/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478580 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 19, 32, 32, 50, 50, 77, 121, 201, 201, 201, 201, 201, 8, 1, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 19, 19, 32, 32, 32, 77, 77, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 526 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478580 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 179, 201, 179, 179, 179, 156, 101, 62, 101, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 156, 156, 101, 101, 101, 29, 29, 1, 179, 179] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 765 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478580 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 14, 14, 32, 32, 59, 92, 179, 179, 179, 179, 179, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 59, 59, 179, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 432 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478580 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478580 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478580/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478580 Building REAL300025478581 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478581' /scratch/stefan/7787258/working/building/REAL300025478581 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478581 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478581/0 /scratch/stefan/7787258/working/building/REAL300025478581 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/465 `/scratch/stefan/7787258/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478581 none CN(CC1CCN(C(=O)CC2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 19, 37, 37, 37, 37, 37, 1, 8, 12, 12, 16, 16, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 16, 16, 43] 148 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478581 none CN(CC1CCN(C(=O)CC2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [36, 35, 36, 39, 43, 43, 43, 43, 54, 54, 126, 148, 148, 148, 148, 148, 43, 31, 35, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 39, 39, 43, 43, 43, 43, 43, 126, 126, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 43, 43, 31, 31, 1] 148 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 590 number of broken/clashed sets: 87 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478581 none CN(CC1CCN(C(=O)CC2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [80, 57, 37, 37, 37, 37, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 37, 80, 105, 105, 114, 114, 148, 148, 148, 148, 148, 80, 80, 80, 57, 57, 37, 37, 37, 37, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 114, 114, 148] 148 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51, 52, 53, 54]) total number of confs: 488 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478581 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478581 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478581/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478581 Building REAL300025478582 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478582' /scratch/stefan/7787258/working/building/REAL300025478582 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478582 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478582/0 /scratch/stefan/7787258/working/building/REAL300025478582 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/466 `/scratch/stefan/7787258/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478582 none CN(CC1CCN(C(=O)C2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 1, 14, 32, 32, 59, 87, 144, 144, 144, 144, 144, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 59, 59, 144] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 396 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: REAL300025478582 none CN(CC1CCN(C(=O)C2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 68, 84, 130, 144, 144, 144, 144, 172, 172, 201, 201, 201, 201, 144, 31, 68, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 130, 130, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 144, 31, 31, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 810 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: REAL300025478582 none CN(CC1CCN(C(=O)C2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 9, 47, 78, 78, 116, 152, 201, 201, 201, 201, 201, 47, 47, 47, 26, 26, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 116, 116, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 613 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478582 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478582 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478582/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478582 Building REAL300025478583 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478583' /scratch/stefan/7787258/working/building/REAL300025478583 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478583 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478583/0 /scratch/stefan/7787258/working/building/REAL300025478583 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/467 `/scratch/stefan/7787258/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478583 none CSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 39, 63, 129, 129, 129, 129, 129, 1, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 39, 39, 129, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 42, 22, 41, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478583 none CSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 154, 129, 154, 129, 129, 129, 120, 80, 52, 80, 23, 52, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 198, 198, 129, 129, 129, 129, 129, 120, 120, 80, 80, 80, 23, 23, 1, 129, 129] 201 rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 860 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478583 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478583 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478583/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478583 Building REAL300025478584 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478584' /scratch/stefan/7787258/working/building/REAL300025478584 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478584 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478584/0 /scratch/stefan/7787258/working/building/REAL300025478584 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/468 `/scratch/stefan/7787258/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1) `REAL300025478584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478584 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 14, 23, 23, 44, 44, 76, 118, 201, 201, 201, 201, 201, 7, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 7, 14, 14, 23, 23, 23, 76, 76, 201, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 530 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478584 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 153, 201, 153, 153, 153, 141, 102, 59, 102, 26, 59, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 141, 141, 102, 102, 102, 26, 26, 1, 153, 153] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 738 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478584 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 12, 12, 28, 28, 51, 83, 153, 153, 153, 153, 153, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 51, 51, 153, 1, 1] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 385 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478584 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478584 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478584/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478584 Building REAL300025478585 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478585' /scratch/stefan/7787258/working/building/REAL300025478585 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478585 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478585/0 /scratch/stefan/7787258/working/building/REAL300025478585 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/469 `/scratch/stefan/7787258/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478585 none CSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 24, 39, 112, 112, 112, 112, 112, 1, 19, 19, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 24, 24, 112, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 277 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478585 none CSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 145, 145, 125, 112, 125, 112, 112, 112, 93, 58, 41, 58, 27, 41, 12, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 145, 145, 145, 145, 112, 112, 112, 112, 112, 93, 93, 58, 58, 58, 27, 27, 1, 112, 112] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 713 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478585 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478585 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478585/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478585 Building REAL300025478586 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478586' /scratch/stefan/7787258/working/building/REAL300025478586 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478586 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478586/0 /scratch/stefan/7787258/working/building/REAL300025478586 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/470 `/scratch/stefan/7787258/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478586 none CC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 14, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 28, 47, 116, 116, 116, 116, 116, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 116, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 300 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478586 none CC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 127, 116, 127, 116, 116, 116, 105, 81, 57, 81, 28, 57, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 105, 105, 81, 81, 81, 28, 28, 1, 116, 116] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 852 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478586 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478586 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478586/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478586 Building REAL300025478587 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478587' /scratch/stefan/7787258/working/building/REAL300025478587 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478587 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478587/0 /scratch/stefan/7787258/working/building/REAL300025478587 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/471 `/scratch/stefan/7787258/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478587 none CN(CC1CCN(C(=O)C2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 1, 11, 25, 25, 47, 66, 118, 118, 118, 118, 118, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 1, 1, 47, 47, 118] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 318 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478587 none CN(CC1CCN(C(=O)C2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 61, 66, 105, 118, 118, 118, 118, 136, 136, 201, 201, 201, 201, 118, 36, 61, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 105, 105, 118, 118, 118, 118, 118, 201, 201, 201, 118, 118, 36, 36, 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: 694 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478587 none CN(CC1CCN(C(=O)C2=CSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 9, 33, 59, 59, 105, 136, 201, 201, 201, 201, 201, 33, 33, 33, 22, 22, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 105, 105, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 606 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478587 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478587 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478587/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478587 Building REAL300025478588 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478588' /scratch/stefan/7787258/working/building/REAL300025478588 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478588 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478588/0 /scratch/stefan/7787258/working/building/REAL300025478588 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/472 `/scratch/stefan/7787258/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1) `REAL300025478588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478588 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 24, 32, 32, 49, 49, 81, 119, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 24, 24, 32, 32, 32, 81, 81, 201, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478588 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 118, 151, 118, 118, 118, 103, 70, 51, 70, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 103, 103, 70, 70, 70, 27, 27, 1, 118, 118, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 691 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478588 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 19, 19, 39, 59, 118, 118, 118, 118, 118, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 39, 39, 118, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 301 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478588 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478588 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478588/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478588 Building REAL300025478589 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478589' /scratch/stefan/7787258/working/building/REAL300025478589 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478589 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478589/0 /scratch/stefan/7787258/working/building/REAL300025478589 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/473 `/scratch/stefan/7787258/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2C=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478589 none CN(CC1CCN(C(=O)CC2C=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 17, 27, 27, 27, 27, 1, 8, 12, 12, 18, 18, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 27, 27, 27, 27, 27, 27, 27, 1, 1, 18, 18, 43] 103 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478589 none CN(CC1CCN(C(=O)CC2C=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 33, 35, 38, 43, 43, 43, 43, 50, 50, 94, 103, 103, 103, 103, 43, 28, 33, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 38, 38, 43, 43, 43, 43, 43, 94, 94, 103, 103, 103, 103, 103, 103, 103, 43, 43, 28, 28, 1] 103 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 417 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478589 none CN(CC1CCN(C(=O)CC2C=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 41, 27, 27, 27, 27, 16, 6, 16, 1, 1, 1, 1, 1, 1, 27, 57, 74, 74, 82, 82, 103, 103, 103, 103, 103, 57, 57, 57, 41, 41, 27, 27, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 82, 82, 103] 103 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 42] 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, 45, 46, 47, 48, 49]) total number of confs: 346 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478589 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478589 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478589/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478589 Building REAL300025478590 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478590' /scratch/stefan/7787258/working/building/REAL300025478590 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478590 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478590/0 /scratch/stefan/7787258/working/building/REAL300025478590 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/474 `/scratch/stefan/7787258/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478590 none CN(CC1CCN(C(=O)CN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 28, 28, 28, 28, 1, 10, 15, 15, 23, 23, 40, 40, 40, 40, 40, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 13, 13, 28, 1, 1, 23, 23, 40] 83 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 181 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: REAL300025478590 none CN(CC1CCN(C(=O)CN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 34, 38, 40, 40, 40, 40, 49, 49, 78, 83, 83, 83, 83, 40, 25, 33, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 38, 38, 40, 40, 40, 40, 40, 78, 78, 83, 40, 40, 25, 25, 1] 83 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 330 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: REAL300025478590 none CN(CC1CCN(C(=O)CN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 28, 28, 28, 28, 20, 9, 20, 1, 1, 1, 1, 1, 1, 28, 49, 53, 53, 68, 68, 83, 83, 83, 83, 83, 49, 49, 49, 38, 38, 28, 28, 28, 28, 28, 9, 9, 1, 28, 28, 68, 68, 83] 83 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43]) total number of confs: 299 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478590 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478590 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478590/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478590 Building REAL300025478591 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478591' /scratch/stefan/7787258/working/building/REAL300025478591 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478591 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478591/0 /scratch/stefan/7787258/working/building/REAL300025478591 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/475 `/scratch/stefan/7787258/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2CCCC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478591 none CN(CC1CCN(C(=O)CN2CCCC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 36, 36, 36, 36, 36, 1, 9, 14, 14, 20, 21, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 36, 36, 36, 36, 36, 36, 1, 1, 20, 20, 50] 145 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478591 none CN(CC1CCN(C(=O)CN2CCCC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [42, 41, 42, 45, 50, 50, 50, 50, 72, 72, 142, 145, 145, 145, 145, 145, 50, 30, 41, 11, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 45, 45, 50, 50, 50, 50, 50, 142, 142, 145, 145, 145, 145, 145, 145, 50, 50, 30, 30, 1] 145 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478591 none CN(CC1CCN(C(=O)CN2CCCC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [76, 56, 36, 36, 36, 36, 25, 7, 25, 1, 1, 1, 1, 1, 1, 1, 36, 76, 94, 94, 105, 105, 145, 145, 145, 145, 145, 76, 76, 76, 56, 56, 36, 36, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 1, 36, 36, 105, 105, 145] 145 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 445 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478591 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478591 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478591/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478591 Building REAL300025478592 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478592' /scratch/stefan/7787258/working/building/REAL300025478592 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478592 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478592/0 /scratch/stefan/7787258/working/building/REAL300025478592 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/476 `/scratch/stefan/7787258/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478592 none CN(CC1CCN(C(=O)C2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 13, 27, 27, 55, 82, 152, 152, 152, 152, 152, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 55, 55, 152] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 386 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478592 none CN(CC1CCN(C(=O)C2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 84, 98, 141, 152, 152, 152, 152, 169, 169, 201, 201, 201, 201, 201, 152, 40, 84, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 141, 141, 152, 152, 152, 152, 152, 201, 201, 201, 201, 201, 152, 152, 40, 40, 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: 732 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478592 none CN(CC1CCN(C(=O)C2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 36, 61, 61, 105, 140, 201, 201, 201, 201, 201, 36, 36, 36, 24, 24, 10, 10, 10, 10, 10, 1, 2, 2, 2, 1, 10, 10, 105, 105, 201] 201 rigid atoms, others: [36, 7, 40, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 610 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478592 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478592 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478592/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478592 Building REAL300025478593 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478593' /scratch/stefan/7787258/working/building/REAL300025478593 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478593 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478593/0 /scratch/stefan/7787258/working/building/REAL300025478593 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/477 `/scratch/stefan/7787258/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478593 none CC1=NOC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 21, 34, 34, 58, 58, 88, 128, 201, 201, 201, 201, 201, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 21, 21, 34, 34, 34, 88, 88, 201, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 580 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: REAL300025478593 none CC1=NOC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 109, 79, 109, 79, 79, 79, 70, 50, 39, 50, 24, 39, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 79, 79, 79, 79, 79, 70, 70, 50, 50, 50, 24, 24, 1, 79, 79] 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, 46, 47]) total number of confs: 605 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: REAL300025478593 none CC1=NOC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 17, 17, 28, 41, 79, 79, 79, 79, 79, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 79, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478593 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478593 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478593/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478593 Building REAL300025478594 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478594' /scratch/stefan/7787258/working/building/REAL300025478594 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478594 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478594/0 /scratch/stefan/7787258/working/building/REAL300025478594 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/478 `/scratch/stefan/7787258/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1) `REAL300025478594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478594 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 27, 37, 37, 53, 53, 83, 122, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 27, 27, 37, 37, 37, 83, 83, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 572 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: REAL300025478594 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 110, 153, 110, 110, 110, 95, 67, 51, 67, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 95, 95, 67, 67, 67, 29, 29, 1, 110, 110] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 676 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: REAL300025478594 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 33, 50, 110, 110, 110, 110, 110, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 33, 33, 110, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 271 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478594 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478594 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478594/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478594 Building REAL300025478595 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478595' /scratch/stefan/7787258/working/building/REAL300025478595 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478595 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478595/0 /scratch/stefan/7787258/working/building/REAL300025478595 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/479 `/scratch/stefan/7787258/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1) `REAL300025478595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478595 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 30, 41, 41, 57, 57, 84, 125, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 30, 30, 41, 41, 41, 84, 84, 201, 11, 11, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 572 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: REAL300025478595 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 127, 151, 127, 127, 127, 106, 71, 50, 71, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 127, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 127, 106, 106, 71, 71, 71, 29, 29, 1, 127, 127, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 690 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: REAL300025478595 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 21, 21, 39, 59, 127, 127, 127, 127, 127, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 39, 39, 127, 1, 1, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478595 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478595 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478595/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478595 Building REAL300025478596 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478596' /scratch/stefan/7787258/working/building/REAL300025478596 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478596 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478596/0 /scratch/stefan/7787258/working/building/REAL300025478596 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/480 `/scratch/stefan/7787258/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478596 none CN(CC1CCN(C(=O)C2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 13, 30, 30, 58, 77, 129, 129, 129, 129, 129, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 58, 58, 129] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 367 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478596 none CN(CC1CCN(C(=O)C2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 62, 74, 112, 129, 129, 129, 129, 143, 143, 201, 201, 201, 201, 201, 129, 36, 62, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 112, 112, 129, 129, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 36, 36, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 815 number of broken/clashed sets: 79 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478596 none CN(CC1CCN(C(=O)C2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 32, 62, 62, 111, 142, 201, 201, 201, 201, 201, 32, 32, 32, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 111, 111, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 611 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478596 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478596 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478596/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478596 Building REAL300025478597 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478597' /scratch/stefan/7787258/working/building/REAL300025478597 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478597 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478597/0 /scratch/stefan/7787258/working/building/REAL300025478597 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/481 `/scratch/stefan/7787258/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478597 none CN(CC1CCN(C(=O)CCC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 18, 25, 47, 47, 47, 47, 1, 8, 12, 12, 19, 20, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 18, 18, 25, 25, 47, 47, 47, 1, 1, 19, 19, 50] 191 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 253 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478597 none CN(CC1CCN(C(=O)CCC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 41, 44, 50, 50, 50, 50, 73, 73, 153, 162, 191, 191, 191, 191, 50, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 44, 44, 50, 50, 50, 50, 50, 153, 153, 162, 162, 191, 191, 191, 50, 50, 33, 33, 1] 191 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 704 number of broken/clashed sets: 106 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478597 none CN(CC1CCN(C(=O)CCC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [99, 74, 47, 47, 47, 47, 27, 9, 27, 4, 1, 1, 1, 1, 1, 1, 47, 99, 128, 128, 145, 145, 191, 191, 191, 191, 191, 99, 99, 99, 74, 74, 47, 47, 47, 47, 47, 9, 9, 4, 4, 1, 1, 1, 47, 47, 145, 145, 191] 191 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 616 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478597 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478597 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478597/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478597 Building REAL300025478598 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478598' /scratch/stefan/7787258/working/building/REAL300025478598 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478598 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478598/0 /scratch/stefan/7787258/working/building/REAL300025478598 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/482 `/scratch/stefan/7787258/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478598 none CC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 16, 27, 27, 49, 49, 79, 118, 201, 201, 201, 201, 201, 6, 1, 2, 2, 2, 6, 6, 7, 7, 7, 16, 16, 27, 27, 27, 79, 79, 201, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 526 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478598 none CC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 172, 201, 172, 172, 172, 156, 111, 65, 111, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 172, 172, 172, 172, 172, 156, 156, 111, 111, 111, 28, 28, 1, 172, 172, 201] 201 rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 743 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478598 none CC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 14, 14, 33, 33, 59, 92, 172, 172, 172, 172, 172, 1, 6, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 59, 59, 172, 1, 1, 7] 201 rigid atoms, others: [32, 33, 43, 5, 7, 8, 9, 10, 11, 42, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 429 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478598 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478598 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478598/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478598 Building REAL300025478599 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478599' /scratch/stefan/7787258/working/building/REAL300025478599 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478599 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478599/0 /scratch/stefan/7787258/working/building/REAL300025478599 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/483 `/scratch/stefan/7787258/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478599 none CN(CC1CCN(C(=O)C2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 1, 13, 27, 27, 51, 74, 136, 136, 136, 136, 136, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 51, 51, 136] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 355 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478599 none CN(CC1CCN(C(=O)C2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 75, 79, 120, 136, 136, 136, 136, 153, 153, 201, 201, 201, 201, 136, 40, 75, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 120, 120, 136, 136, 136, 136, 136, 201, 201, 201, 201, 136, 136, 40, 40, 1] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 705 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478599 none CN(CC1CCN(C(=O)C2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 11, 38, 64, 64, 108, 135, 201, 201, 201, 201, 201, 38, 38, 38, 26, 26, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 108, 108, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 595 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478599 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478599 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478599/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478599 Building REAL300025478600 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478600' /scratch/stefan/7787258/working/building/REAL300025478600 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478600 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478600/0 /scratch/stefan/7787258/working/building/REAL300025478600 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/484 `/scratch/stefan/7787258/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(Cl)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478600 none CN(CC1CCN(C(=O)C2=CC(Cl)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 1, 15, 28, 28, 54, 74, 142, 142, 142, 142, 142, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 13, 13, 13, 1, 1, 54, 54, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 370 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478600 none CN(CC1CCN(C(=O)C2=CC(Cl)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 81, 84, 125, 142, 142, 142, 142, 161, 161, 201, 201, 201, 201, 201, 142, 39, 81, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 125, 125, 142, 142, 142, 142, 142, 201, 201, 201, 142, 142, 39, 39, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 714 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478600 none CN(CC1CCN(C(=O)C2=CC(Cl)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 27, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 44, 67, 67, 112, 138, 201, 201, 201, 201, 201, 44, 44, 44, 27, 27, 13, 13, 13, 13, 13, 1, 1, 1, 13, 13, 112, 112, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 598 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478600 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478600 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478600/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478600 Building REAL300025478601 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478601' /scratch/stefan/7787258/working/building/REAL300025478601 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478601 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478601/0 /scratch/stefan/7787258/working/building/REAL300025478601 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/485 `/scratch/stefan/7787258/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478601 none CC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 20, 40, 14, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 6, 6, 7, 7, 15, 24, 80, 80, 80, 80, 80, 1, 40, 40, 40, 19, 18, 17, 17, 12, 12, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 15, 15, 80, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 313 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478601 none CC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 201, 160, 165, 84, 80, 84, 80, 80, 80, 68, 43, 36, 43, 25, 36, 11, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 174, 173, 173, 173, 165, 165, 80, 80, 80, 80, 80, 68, 68, 43, 43, 43, 25, 25, 1, 80, 80] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 922 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478601 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478601 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478601/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478601 Building REAL300025478602 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478602' /scratch/stefan/7787258/working/building/REAL300025478602 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478602 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478602/0 /scratch/stefan/7787258/working/building/REAL300025478602 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/486 `/scratch/stefan/7787258/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1C) `REAL300025478602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478602 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 25, 34, 34, 55, 55, 83, 122, 201, 201, 201, 201, 201, 9, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 25, 25, 34, 34, 34, 83, 83, 201, 9, 9, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 565 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478602 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 122, 160, 122, 122, 122, 105, 72, 52, 72, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 105, 105, 72, 72, 72, 28, 28, 1, 122, 122, 201, 201, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 693 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478602 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 23, 23, 40, 61, 122, 122, 122, 122, 122, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 40, 40, 122, 1, 1, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 309 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478602 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478602 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478602/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478602 Building REAL300025478603 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478603' /scratch/stefan/7787258/working/building/REAL300025478603 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478603 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478603/0 /scratch/stefan/7787258/working/building/REAL300025478603 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/487 `/scratch/stefan/7787258/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478603 none CN(CC1CCN(C(=O)C2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 1, 13, 28, 28, 49, 70, 126, 126, 126, 126, 126, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 49, 49, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 336 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: REAL300025478603 none CN(CC1CCN(C(=O)C2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 75, 80, 113, 126, 126, 126, 126, 147, 147, 201, 201, 201, 201, 126, 40, 75, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 113, 113, 126, 126, 126, 126, 126, 201, 201, 201, 126, 126, 40, 40, 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: 690 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: REAL300025478603 none CN(CC1CCN(C(=O)C2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 11, 41, 68, 68, 107, 140, 201, 201, 201, 201, 201, 41, 41, 41, 26, 26, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 107, 107, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 598 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478603 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478603 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478603/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478603 Building REAL300025478604 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478604' /scratch/stefan/7787258/working/building/REAL300025478604 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478604 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478604/0 /scratch/stefan/7787258/working/building/REAL300025478604 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/488 `/scratch/stefan/7787258/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478604 none CN(CC1CCN(C(=O)CN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 38, 38, 38, 38, 1, 10, 15, 15, 24, 26, 52, 52, 52, 52, 52, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 21, 21, 38, 38, 38, 1, 1, 24, 24, 52] 144 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 230 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: REAL300025478604 none CN(CC1CCN(C(=O)CN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [40, 38, 40, 48, 52, 52, 52, 52, 80, 80, 135, 144, 144, 144, 144, 52, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 48, 48, 52, 52, 52, 52, 52, 135, 135, 144, 144, 144, 52, 52, 29, 29, 1] 144 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: 585 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: REAL300025478604 none CN(CC1CCN(C(=O)CN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [78, 59, 38, 38, 38, 38, 19, 9, 19, 1, 1, 1, 1, 1, 1, 38, 78, 96, 96, 114, 116, 144, 144, 144, 144, 144, 78, 78, 78, 59, 59, 38, 38, 38, 38, 38, 9, 9, 1, 1, 1, 38, 38, 114, 114, 144] 144 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 481 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478604 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478604 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478604/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478604 Building REAL300025478605 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478605' /scratch/stefan/7787258/working/building/REAL300025478605 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478605 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478605/0 /scratch/stefan/7787258/working/building/REAL300025478605 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/489 `/scratch/stefan/7787258/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1) `REAL300025478605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478605 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 23, 31, 31, 52, 52, 81, 122, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 23, 23, 31, 31, 31, 81, 81, 201, 11, 11, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 559 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: REAL300025478605 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 109, 146, 109, 109, 109, 100, 68, 49, 68, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 109, 100, 100, 68, 68, 68, 28, 28, 1, 109, 109, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 665 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: REAL300025478605 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 37, 55, 109, 109, 109, 109, 109, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 37, 37, 109, 1, 1, 11, 11] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 286 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478605 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478605 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478605/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478605 Building REAL300025478606 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478606' /scratch/stefan/7787258/working/building/REAL300025478606 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478606 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478606/0 /scratch/stefan/7787258/working/building/REAL300025478606 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/490 `/scratch/stefan/7787258/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC3CCC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478606 none CN(CC1CCN(C(=O)C2CC3CCC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 1, 16, 37, 37, 79, 103, 182, 182, 182, 182, 182, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 79, 79, 182] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 490 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: REAL300025478606 none CN(CC1CCN(C(=O)C2CC3CCC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 77, 105, 155, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 182, 40, 77, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 155, 155, 182, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 40, 40, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 804 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: REAL300025478606 none CN(CC1CCN(C(=O)C2CC3CCC2C3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 30, 60, 60, 107, 136, 201, 201, 201, 201, 201, 30, 30, 30, 14, 14, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 585 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478606 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478606 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478606/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478606 Building REAL300025478607 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478607' /scratch/stefan/7787258/working/building/REAL300025478607 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478607 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478607/0 /scratch/stefan/7787258/working/building/REAL300025478607 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/491 `/scratch/stefan/7787258/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(Cl)O2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478607 none CN(CC1CCN(C(=O)C2=CC=C(Cl)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 7, 7, 7, 1, 13, 30, 30, 52, 80, 157, 157, 157, 157, 157, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 6, 6, 1, 1, 52, 52, 157] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 15, 35, 38, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 40, 41, 42]) total number of confs: 382 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478607 none CN(CC1CCN(C(=O)C2=CC=C(Cl)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 80, 131, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 157, 35, 69, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 131, 131, 157, 157, 157, 157, 157, 201, 201, 157, 157, 35, 35, 1] 201 rigid atoms, others: [42, 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: 808 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478607 none CN(CC1CCN(C(=O)C2=CC=C(Cl)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 20, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 32, 59, 59, 96, 139, 201, 201, 201, 201, 201, 32, 32, 32, 20, 20, 7, 7, 7, 7, 7, 1, 1, 6, 6, 96, 96, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 558 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478607 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478607 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478607/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478607 Building REAL300025478608 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478608' /scratch/stefan/7787258/working/building/REAL300025478608 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478608 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478608/0 /scratch/stefan/7787258/working/building/REAL300025478608 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/492 `/scratch/stefan/7787258/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C) `REAL300025478608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478608 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 29, 43, 43, 58, 58, 85, 122, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 29, 29, 43, 43, 43, 85, 85, 201, 10, 10, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 45, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 585 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478608 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 132, 167, 132, 132, 132, 108, 76, 60, 76, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 108, 108, 76, 76, 76, 28, 28, 1, 132, 132, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 693 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478608 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 41, 59, 132, 132, 132, 132, 132, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 41, 41, 132, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 325 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478608 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478608 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478608/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478608 Building REAL300025478609 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478609' /scratch/stefan/7787258/working/building/REAL300025478609 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478609 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478609/0 /scratch/stefan/7787258/working/building/REAL300025478609 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/493 `/scratch/stefan/7787258/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478609 none CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 13, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 25, 40, 98, 98, 98, 98, 98, 1, 14, 14, 14, 13, 13, 14, 14, 13, 13, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 25, 25, 98, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 271 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478609 none CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 198, 109, 98, 109, 98, 98, 98, 87, 62, 47, 62, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 98, 98, 98, 98, 98, 87, 87, 62, 62, 62, 26, 26, 1, 98, 98] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 884 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478609 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478609 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478609/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478609 Building REAL300025478610 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478610' /scratch/stefan/7787258/working/building/REAL300025478610 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478610 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478610/0 /scratch/stefan/7787258/working/building/REAL300025478610 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/494 `/scratch/stefan/7787258/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478610 none CN(CC1CCN(C(=O)CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 1, 1, 1, 1, 1, 1, 7, 7, 11, 14, 14, 14, 1, 9, 14, 14, 21, 21, 51, 51, 51, 51, 51, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 21, 21, 51] 81 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 47, 46, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 169 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478610 none CN(CC1CCN(C(=O)CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 42, 43, 45, 51, 51, 51, 51, 64, 64, 81, 81, 81, 81, 51, 32, 42, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 45, 45, 51, 51, 51, 51, 51, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 51, 51, 32, 32, 1] 81 rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 318 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478610 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478610 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478610/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478610 Building REAL300025478611 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478611' /scratch/stefan/7787258/working/building/REAL300025478611 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478611 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478611/0 /scratch/stefan/7787258/working/building/REAL300025478611 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/495 `/scratch/stefan/7787258/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1) `REAL300025478611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478611 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 29, 40, 40, 46, 46, 75, 115, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 29, 29, 40, 40, 40, 75, 75, 201, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 528 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478611 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 154, 161, 154, 154, 154, 126, 88, 62, 88, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 126, 126, 88, 88, 88, 28, 28, 1, 154, 154, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 699 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478611 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 20, 20, 43, 71, 154, 154, 154, 154, 154, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 43, 43, 154, 1, 1, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 370 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478611 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478611 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478611/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478611 Building REAL300025478612 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478612' /scratch/stefan/7787258/working/building/REAL300025478612 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478612 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478612/0 /scratch/stefan/7787258/working/building/REAL300025478612 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/496 `/scratch/stefan/7787258/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478612 none CN(CC1CCN(C(=O)C2=CC=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 1, 13, 28, 28, 54, 75, 123, 123, 123, 123, 123, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 54, 54, 123] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 347 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478612 none CN(CC1CCN(C(=O)C2=CC=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 59, 72, 110, 123, 123, 123, 123, 169, 169, 201, 201, 201, 201, 201, 123, 32, 59, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 110, 110, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201, 201, 123, 123, 32, 32, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 746 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478612 none CN(CC1CCN(C(=O)C2=CC=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 23, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 41, 69, 69, 113, 148, 201, 201, 201, 201, 201, 41, 41, 41, 23, 23, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2, 8, 8, 113, 113, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 618 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478612 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478612 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478612/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478612 Building REAL300025478613 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478613' /scratch/stefan/7787258/working/building/REAL300025478613 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478613 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478613/0 /scratch/stefan/7787258/working/building/REAL300025478613 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/497 `/scratch/stefan/7787258/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478613 none CN(CC1CCN(C(=O)CCN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 29, 52, 52, 52, 52, 1, 11, 16, 16, 24, 25, 54, 54, 54, 54, 54, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 21, 21, 29, 29, 52, 52, 1, 1, 24, 24, 54] 180 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 290 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478613 none CN(CC1CCN(C(=O)CCN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [44, 42, 44, 47, 54, 54, 54, 54, 78, 78, 156, 168, 180, 180, 180, 180, 54, 32, 42, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 47, 47, 54, 54, 54, 54, 54, 156, 156, 168, 168, 180, 180, 54, 54, 32, 32, 1] 180 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 731 number of broken/clashed sets: 94 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478613 none CN(CC1CCN(C(=O)CCN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [103, 77, 52, 52, 52, 52, 30, 12, 30, 7, 1, 1, 1, 1, 1, 1, 52, 103, 128, 128, 146, 146, 180, 180, 180, 180, 180, 103, 103, 103, 77, 77, 52, 52, 52, 52, 52, 12, 12, 7, 7, 1, 1, 52, 52, 146, 146, 180] 180 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 609 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478613 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478613 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478613/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478613 Building REAL300025478614 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478614' /scratch/stefan/7787258/working/building/REAL300025478614 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478614 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478614/0 /scratch/stefan/7787258/working/building/REAL300025478614 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/498 `/scratch/stefan/7787258/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478614 none CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 26, 40, 107, 107, 107, 107, 107, 1, 14, 14, 14, 13, 13, 13, 13, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 26, 26, 107, 1, 1] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 285 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478614 none CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 121, 107, 121, 107, 107, 107, 94, 62, 46, 62, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 198, 198, 107, 107, 107, 107, 107, 94, 94, 62, 62, 62, 26, 26, 1, 107, 107] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 873 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478614 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478614 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478614/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478614 Building REAL300025478615 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478615' /scratch/stefan/7787258/working/building/REAL300025478615 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478615 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478615/0 /scratch/stefan/7787258/working/building/REAL300025478615 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/499 `/scratch/stefan/7787258/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478615 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 23, 31, 31, 51, 51, 83, 121, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 31, 31, 31, 83, 83, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 569 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478615 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 173, 143, 173, 143, 143, 143, 127, 93, 64, 93, 27, 64, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 127, 127, 93, 93, 93, 27, 27, 1, 143, 143] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 685 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478615 none CC1=CC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 25, 25, 48, 72, 143, 143, 143, 143, 143, 1, 9, 10, 10, 10, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 48, 48, 143, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 377 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478615 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478615 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478615/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478615 Building REAL300025478616 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478616' /scratch/stefan/7787258/working/building/REAL300025478616 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478616 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478616/0 /scratch/stefan/7787258/working/building/REAL300025478616 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/500 `/scratch/stefan/7787258/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478616 none CC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 33, 33, 68, 95, 185, 185, 185, 185, 185, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 68, 68, 185, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 482 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: REAL300025478616 none CC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 201, 185, 185, 185, 159, 107, 81, 107, 38, 81, 13, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185, 185, 159, 159, 107, 107, 107, 38, 38, 1, 185, 185] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 808 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478616 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478616 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478616/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478616 Building REAL300025478617 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478617' /scratch/stefan/7787258/working/building/REAL300025478617 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478617 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478617/0 /scratch/stefan/7787258/working/building/REAL300025478617 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/501 `/scratch/stefan/7787258/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478617 none CN(CC1CCN(C(=O)CCN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 26, 45, 45, 45, 45, 1, 9, 14, 14, 21, 21, 48, 48, 48, 48, 48, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 17, 17, 26, 26, 45, 45, 45, 1, 1, 21, 21, 48] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 255 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478617 none CN(CC1CCN(C(=O)CCN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 38, 40, 43, 48, 48, 48, 48, 65, 65, 167, 178, 201, 201, 201, 201, 48, 31, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 43, 43, 48, 48, 48, 48, 48, 167, 167, 178, 178, 201, 201, 201, 48, 48, 31, 31, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 776 number of broken/clashed sets: 102 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478617 none CN(CC1CCN(C(=O)CCN2C=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 72, 45, 45, 45, 45, 29, 11, 29, 6, 1, 1, 1, 1, 1, 1, 45, 102, 132, 132, 144, 144, 201, 201, 201, 201, 201, 102, 102, 102, 72, 72, 45, 45, 45, 45, 45, 11, 11, 6, 6, 1, 1, 1, 45, 45, 144, 144, 201] 201 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 636 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478617 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478617 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478617/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478617 Building REAL300025478618 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478618' /scratch/stefan/7787258/working/building/REAL300025478618 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478618 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478618/0 /scratch/stefan/7787258/working/building/REAL300025478618 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/502 `/scratch/stefan/7787258/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478618 none CN(CC1CCN(C(=O)C2=CC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 6, 9, 9, 9, 1, 12, 32, 32, 64, 90, 168, 168, 168, 168, 168, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 1, 1, 64, 64, 168] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 467 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478618 none CN(CC1CCN(C(=O)C2=CC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [101, 77, 101, 147, 168, 168, 168, 168, 197, 197, 201, 201, 201, 201, 201, 201, 168, 34, 77, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 147, 147, 168, 168, 168, 168, 168, 201, 201, 201, 201, 402, 168, 168, 34, 34, 1] 402 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1198 number of broken/clashed sets: 124 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478618 none CN(CC1CCN(C(=O)C2=CC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 33, 62, 62, 105, 139, 201, 201, 201, 201, 201, 33, 33, 33, 21, 21, 9, 9, 9, 9, 9, 1, 1, 1, 1, 2, 9, 9, 105, 105, 201] 402 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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: 585 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478618 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478618 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478618/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478618 Building REAL300025478619 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478619' /scratch/stefan/7787258/working/building/REAL300025478619 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478619 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478619/0 /scratch/stefan/7787258/working/building/REAL300025478619 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/503 `/scratch/stefan/7787258/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478619 none CCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 22, 22, 50, 84, 176, 176, 176, 176, 176, 1, 8, 8, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 50, 50, 176, 1, 1] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 435 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478619 none CCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 201, 176, 197, 176, 176, 176, 160, 107, 70, 107, 30, 70, 13, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 176, 160, 160, 107, 107, 107, 30, 30, 1, 176, 176] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 771 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478619 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478619 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478619/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478619 Building REAL300025478620 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478620' /scratch/stefan/7787258/working/building/REAL300025478620 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478620 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478620/0 /scratch/stefan/7787258/working/building/REAL300025478620 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/504 `/scratch/stefan/7787258/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478620 none CC(C)SCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 22, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 27, 41, 106, 106, 106, 106, 106, 1, 22, 22, 22, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 27, 27, 106, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 312 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478620 none CC(C)SCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 178, 130, 106, 130, 106, 106, 106, 91, 60, 45, 60, 25, 45, 13, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 178, 178, 106, 106, 106, 106, 106, 91, 91, 60, 60, 60, 25, 25, 1, 106, 106] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 884 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478620 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478620 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478620/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478620 Building REAL300025478621 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478621' /scratch/stefan/7787258/working/building/REAL300025478621 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478621 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478621/0 /scratch/stefan/7787258/working/building/REAL300025478621 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/505 `/scratch/stefan/7787258/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CSCC#N)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478621 none CN(CC1CCN(C(=O)CSCC#N)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 15, 36, 61, 61, 1, 10, 15, 15, 23, 23, 44, 44, 44, 44, 44, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 15, 15, 61, 61, 1, 1, 23, 23, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 319 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478621 none CN(CC1CCN(C(=O)CSCC#N)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 34, 35, 39, 44, 44, 44, 44, 62, 62, 136, 163, 201, 201, 44, 27, 34, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 39, 39, 44, 44, 44, 44, 44, 136, 136, 201, 201, 44, 44, 27, 27, 1] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 807 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478621 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478621 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478621/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478621 Building REAL300025478622 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478622' /scratch/stefan/7787258/working/building/REAL300025478622 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478622 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478622/0 /scratch/stefan/7787258/working/building/REAL300025478622 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/506 `/scratch/stefan/7787258/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478622 none CC(=O)N(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 13, 15, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 31, 48, 120, 120, 120, 120, 120, 1, 15, 15, 15, 15, 15, 15, 13, 13, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 31, 31, 120, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 315 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478622 none CC(=O)N(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 145, 120, 145, 120, 120, 120, 102, 80, 59, 80, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 102, 102, 80, 80, 80, 29, 29, 1, 120, 120] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 800 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478622 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478622 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478622/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478622 Building REAL300025478623 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478623' /scratch/stefan/7787258/working/building/REAL300025478623 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478623 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478623/0 /scratch/stefan/7787258/working/building/REAL300025478623 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/507 `/scratch/stefan/7787258/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478623 none CCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 3, 6, 7, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 30, 30, 59, 95, 168, 168, 168, 168, 168, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 59, 59, 168, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 448 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478623 none CCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 185, 200, 201, 168, 185, 168, 168, 168, 155, 103, 61, 103, 30, 61, 13, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 201, 200, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 155, 155, 103, 103, 103, 30, 30, 1, 168, 168] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 792 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478623 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478623 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478623/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478623 Building REAL300025478624 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478624' /scratch/stefan/7787258/working/building/REAL300025478624 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478624 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478624/0 /scratch/stefan/7787258/working/building/REAL300025478624 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/508 `/scratch/stefan/7787258/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478624 none CC(C)OCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 40, 57, 18, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 18, 18, 24, 31, 73, 73, 73, 73, 73, 1, 57, 57, 57, 57, 57, 57, 57, 18, 18, 14, 14, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 24, 24, 73, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 364 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: REAL300025478624 none CC(C)OCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 156, 151, 87, 73, 87, 73, 73, 73, 61, 49, 35, 49, 17, 35, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 156, 156, 151, 151, 73, 73, 73, 73, 73, 61, 61, 49, 49, 49, 17, 17, 1, 73, 73] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 695 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478624 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478624 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478624/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478624 Building REAL300025478625 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478625' /scratch/stefan/7787258/working/building/REAL300025478625 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478625 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478625/0 /scratch/stefan/7787258/working/building/REAL300025478625 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/509 `/scratch/stefan/7787258/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478625 none CCC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 15, 20, 20, 22, 22, 43, 60, 119, 119, 119, 119, 119, 7, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 7, 15, 15, 20, 20, 20, 43, 43, 119, 7, 7, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 322 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478625 none CCC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 119, 119, 119, 93, 72, 93, 72, 72, 72, 58, 42, 29, 42, 21, 29, 12, 1, 1, 1, 1, 1, 1, 1, 72, 119, 201, 201, 201, 201, 201, 119, 72, 72, 72, 72, 72, 58, 58, 42, 42, 42, 21, 21, 1, 72, 72, 119] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 900 number of broken/clashed sets: 101 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478625 none CCC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 21, 30, 72, 72, 72, 72, 72, 1, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 21, 21, 72, 1, 1, 7] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 222 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478625 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478625/1 /scratch/stefan/7787258/working/building/REAL300025478625 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/510 `/scratch/stefan/7787258/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1) `REAL300025478625.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478625 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 13, 19, 19, 24, 24, 39, 62, 122, 122, 122, 122, 122, 6, 1, 1, 3, 3, 3, 3, 3, 1, 6, 6, 6, 6, 6, 13, 13, 19, 19, 19, 39, 39, 122, 6, 6, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 313 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478625 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 122, 122, 122, 119, 103, 119, 103, 103, 103, 96, 77, 59, 77, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 103, 122, 122, 201, 201, 201, 201, 201, 122, 103, 103, 103, 103, 103, 96, 96, 77, 77, 77, 27, 27, 1, 103, 103, 122] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 918 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478625 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 25, 41, 103, 103, 103, 103, 103, 1, 6, 6, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 103, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 265 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478625 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478625 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478625/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478625/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478625 Building REAL300025478626 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478626' /scratch/stefan/7787258/working/building/REAL300025478626 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478626 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478626/0 /scratch/stefan/7787258/working/building/REAL300025478626 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/511 `/scratch/stefan/7787258/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478626 none CN(CC1CCN(C(=O)CCC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 16, 18, 28, 28, 28, 28, 1, 8, 11, 11, 14, 14, 37, 37, 37, 37, 37, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 21, 21, 28, 28, 28, 28, 28, 28, 28, 1, 1, 14, 14, 37] 104 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 197 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478626 none CN(CC1CCN(C(=O)CCC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 30, 32, 34, 37, 37, 37, 37, 46, 46, 93, 95, 104, 104, 104, 104, 37, 27, 30, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 37, 37, 37, 37, 37, 93, 93, 98, 98, 104, 104, 104, 104, 104, 104, 104, 37, 37, 27, 27, 1] 104 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 451 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478626 none CN(CC1CCN(C(=O)CCC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 40, 28, 28, 28, 28, 19, 9, 19, 5, 1, 1, 1, 1, 1, 1, 28, 56, 71, 71, 76, 76, 104, 104, 104, 104, 104, 56, 56, 56, 40, 40, 28, 28, 28, 28, 28, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 76, 76, 104] 104 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52]) total number of confs: 338 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478626 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478626 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478626/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478626 Building REAL300025478627 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478627' /scratch/stefan/7787258/working/building/REAL300025478627 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478627 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478627/0 /scratch/stefan/7787258/working/building/REAL300025478627 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/512 `/scratch/stefan/7787258/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478627 none CN(CC1CCN(C(=O)C2COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 15, 33, 33, 70, 102, 176, 176, 176, 176, 176, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 70, 70, 176] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 463 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478627 none CN(CC1CCN(C(=O)C2COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 72, 93, 155, 176, 176, 176, 176, 201, 201, 201, 201, 201, 201, 201, 176, 35, 72, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 155, 155, 176, 176, 176, 176, 176, 201, 201, 201, 201, 201, 201, 201, 176, 176, 35, 35, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 831 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478627 none CN(CC1CCN(C(=O)C2COCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 31, 56, 56, 106, 144, 201, 201, 201, 201, 201, 31, 31, 31, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 106, 106, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 594 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478627 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478627 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478627/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478627 Building REAL300025478628 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478628' /scratch/stefan/7787258/working/building/REAL300025478628 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478628 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478628/0 /scratch/stefan/7787258/working/building/REAL300025478628 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/513 `/scratch/stefan/7787258/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478628 none CN(CC1CCN(C(=O)C2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 1, 13, 31, 31, 56, 82, 154, 154, 154, 154, 154, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 4, 4, 3, 1, 1, 56, 56, 154] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 385 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: REAL300025478628 none CN(CC1CCN(C(=O)C2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 80, 89, 139, 154, 154, 154, 154, 201, 201, 201, 201, 201, 201, 154, 36, 80, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 139, 139, 154, 154, 154, 154, 154, 201, 201, 201, 154, 154, 36, 36, 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: 803 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: REAL300025478628 none CN(CC1CCN(C(=O)C2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 4, 4, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 4, 25, 56, 56, 90, 128, 201, 201, 201, 201, 201, 25, 25, 25, 13, 13, 4, 3, 4, 3, 3, 1, 1, 1, 4, 4, 90, 90, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 540 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478628 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478628/1 /scratch/stefan/7787258/working/building/REAL300025478628 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/514 `/scratch/stefan/7787258/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478628 none CN(CC1CCN(C(=O)C2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 1, 13, 24, 24, 49, 69, 120, 120, 120, 120, 120, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 1, 1, 49, 49, 120] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 334 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478628 none CN(CC1CCN(C(=O)C2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 63, 67, 103, 120, 120, 120, 120, 139, 139, 201, 201, 201, 201, 120, 36, 63, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 103, 103, 120, 120, 120, 120, 120, 201, 201, 201, 120, 120, 36, 36, 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: 691 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478628 none CN(CC1CCN(C(=O)C2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 29, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 14, 42, 61, 61, 106, 136, 201, 201, 201, 201, 201, 42, 42, 42, 29, 29, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 106, 106, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 605 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478628 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478628 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478628/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478628/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478628 Building REAL300025478629 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478629' /scratch/stefan/7787258/working/building/REAL300025478629 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478629 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478629/0 /scratch/stefan/7787258/working/building/REAL300025478629 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/515 `/scratch/stefan/7787258/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1) `REAL300025478629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478629 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 24, 24, 44, 73, 145, 145, 145, 145, 145, 1, 5, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 44, 44, 145, 1, 1, 8, 8, 8] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 366 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478629 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 6, 8, 8, 8, 8, 20, 29, 29, 48, 48, 75, 117, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 8, 8, 20, 20, 29, 29, 29, 75, 75, 201, 8, 8, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 541 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478629 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 145, 196, 145, 145, 145, 131, 79, 52, 79, 25, 52, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 131, 131, 79, 79, 79, 25, 25, 1, 145, 145, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 789 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478629 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478629 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478629/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478629 Building REAL300025478630 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478630' /scratch/stefan/7787258/working/building/REAL300025478630 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478630 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478630/0 /scratch/stefan/7787258/working/building/REAL300025478630 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/516 `/scratch/stefan/7787258/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478630 none CCCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 39, 65, 145, 145, 145, 145, 145, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 39, 39, 145, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 363 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478630 none CCCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 182, 157, 182, 182, 145, 157, 145, 145, 145, 127, 87, 52, 87, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 145, 145, 145, 145, 145, 127, 127, 87, 87, 87, 26, 26, 1, 145, 145] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 847 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478630 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478630 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478630/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478630 Building REAL300025478631 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478631' /scratch/stefan/7787258/working/building/REAL300025478631 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478631 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478631/0 /scratch/stefan/7787258/working/building/REAL300025478631 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/517 `/scratch/stefan/7787258/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478631 none CSC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 23, 23, 46, 76, 154, 154, 154, 154, 154, 1, 9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 46, 46, 154, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 389 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478631 none CSC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 193, 193, 154, 193, 154, 154, 154, 141, 87, 56, 87, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 193, 193, 193, 193, 154, 154, 154, 154, 154, 141, 141, 87, 87, 87, 27, 27, 1, 154, 154] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 758 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478631 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478631 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478631/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478631 Building REAL300025478632 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478632' /scratch/stefan/7787258/working/building/REAL300025478632 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478632 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478632/0 /scratch/stefan/7787258/working/building/REAL300025478632 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/518 `/scratch/stefan/7787258/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478632 none CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 43, 72, 152, 152, 152, 152, 152, 1, 10, 10, 10, 10, 10, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 43, 43, 152, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 383 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478632 none CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 161, 187, 152, 161, 152, 152, 152, 126, 87, 58, 87, 27, 58, 12, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 187, 187, 187, 187, 152, 152, 152, 152, 152, 126, 126, 87, 87, 87, 27, 27, 1, 152, 152] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 796 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478632 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478632 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478632/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478632 Building REAL300025478633 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478633' /scratch/stefan/7787258/working/building/REAL300025478633 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478633 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478633/0 /scratch/stefan/7787258/working/building/REAL300025478633 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/519 `/scratch/stefan/7787258/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478633 none CC(C)COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 62, 77, 37, 14, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 23, 28, 62, 62, 62, 62, 62, 1, 77, 77, 77, 77, 77, 77, 77, 62, 62, 14, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 62, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 442 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478633 none CC(C)COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 176, 126, 126, 76, 62, 76, 62, 62, 62, 52, 42, 32, 42, 15, 32, 11, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 62, 62, 62, 62, 62, 52, 52, 42, 42, 42, 15, 15, 1, 62, 62] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 733 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478633 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478633 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478633/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478633 Building REAL300025478634 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478634' /scratch/stefan/7787258/working/building/REAL300025478634 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478634 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478634/0 /scratch/stefan/7787258/working/building/REAL300025478634 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/520 `/scratch/stefan/7787258/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478634 none CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 50, 19, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 17, 21, 39, 39, 39, 39, 39, 1, 75, 75, 75, 74, 74, 46, 46, 23, 23, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 17, 17, 39, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 385 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478634 none CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 127, 121, 45, 39, 45, 39, 39, 39, 30, 28, 23, 28, 13, 23, 9, 1, 1, 1, 1, 1, 1, 1, 39, 201, 201, 201, 201, 201, 190, 192, 142, 142, 121, 121, 39, 39, 39, 39, 39, 30, 30, 28, 28, 28, 13, 13, 1, 39, 39] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 913 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478634 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478634 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478634/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478634 Building REAL300025478635 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478635' /scratch/stefan/7787258/working/building/REAL300025478635 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478635 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478635/0 /scratch/stefan/7787258/working/building/REAL300025478635 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/521 `/scratch/stefan/7787258/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)COCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478635 none CN(CC1CCN(C(=O)COCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 32, 59, 59, 1, 8, 10, 10, 12, 12, 38, 38, 38, 38, 38, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 32, 32, 59, 59, 59, 59, 59, 1, 1, 12, 12, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 277 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: REAL300025478635 none CN(CC1CCN(C(=O)COCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 32, 34, 38, 38, 38, 38, 58, 58, 102, 131, 153, 201, 201, 38, 28, 31, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 38, 38, 38, 38, 38, 102, 102, 153, 153, 201, 201, 201, 201, 201, 38, 38, 28, 28, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 804 number of broken/clashed sets: 98 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478635 none CN(CC1CCN(C(=O)COCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 59, 59, 59, 59, 45, 36, 45, 18, 8, 1, 1, 1, 1, 59, 113, 139, 139, 148, 148, 201, 201, 201, 201, 201, 113, 113, 113, 81, 81, 59, 59, 59, 59, 59, 36, 36, 8, 8, 1, 1, 1, 1, 1, 59, 59, 148, 148, 201] 201 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 665 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478635 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478635 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478635/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478635 Building REAL300025478636 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478636' /scratch/stefan/7787258/working/building/REAL300025478636 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478636 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478636/0 /scratch/stefan/7787258/working/building/REAL300025478636 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/522 `/scratch/stefan/7787258/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478636 none CN(CC1CCN(C(=O)CC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 31, 31, 31, 31, 1, 9, 14, 14, 22, 22, 49, 49, 49, 49, 49, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 16, 16, 31, 31, 31, 31, 31, 31, 31, 1, 1, 22, 22, 49] 139 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 229 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478636 none CN(CC1CCN(C(=O)CC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 38, 40, 44, 49, 49, 49, 49, 68, 68, 128, 139, 139, 139, 139, 49, 31, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 44, 44, 49, 49, 49, 49, 49, 128, 128, 139, 139, 139, 139, 139, 139, 139, 49, 49, 31, 31, 1] 139 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 585 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478636 none CN(CC1CCN(C(=O)CC2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 50, 31, 31, 31, 31, 20, 7, 20, 1, 1, 1, 1, 1, 1, 31, 74, 92, 92, 105, 105, 139, 139, 139, 139, 139, 74, 74, 74, 50, 50, 31, 31, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 105, 105, 139] 139 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 42] 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, 45, 46, 47, 48, 49]) total number of confs: 458 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478636 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478636 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478636/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478636 Building REAL300025478637 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478637' /scratch/stefan/7787258/working/building/REAL300025478637 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478637 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478637/0 /scratch/stefan/7787258/working/building/REAL300025478637 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/523 `/scratch/stefan/7787258/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1) `REAL300025478637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478637 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 25, 37, 37, 53, 53, 82, 119, 201, 201, 201, 201, 201, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 25, 25, 37, 37, 37, 82, 82, 201, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 574 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: REAL300025478637 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 124, 154, 124, 124, 124, 106, 76, 56, 76, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 106, 106, 76, 76, 76, 29, 29, 1, 124, 124, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 676 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: REAL300025478637 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 40, 56, 124, 124, 124, 124, 124, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 40, 40, 124, 1, 1, 8] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 311 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478637 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478637 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478637/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478637 Building REAL300025478638 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478638' /scratch/stefan/7787258/working/building/REAL300025478638 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478638 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478638/0 /scratch/stefan/7787258/working/building/REAL300025478638 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/524 `/scratch/stefan/7787258/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478638 none CN(CC1CCN(C(=O)C2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 1, 14, 33, 33, 65, 91, 156, 156, 156, 156, 156, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 65, 65, 156] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 418 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: REAL300025478638 none CN(CC1CCN(C(=O)C2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 73, 88, 140, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 156, 36, 73, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 140, 140, 156, 156, 156, 156, 156, 201, 201, 201, 156, 156, 36, 36, 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: 816 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: REAL300025478638 none CN(CC1CCN(C(=O)C2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 21, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 36, 60, 60, 96, 132, 201, 201, 201, 201, 201, 36, 36, 36, 21, 21, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 96, 96, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 566 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478638 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478638 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478638/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478638 Building REAL300025478639 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478639' /scratch/stefan/7787258/working/building/REAL300025478639 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478639 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478639/0 /scratch/stefan/7787258/working/building/REAL300025478639 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/525 `/scratch/stefan/7787258/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CNC(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478639 none CN(CC1CCN(C(=O)CNC(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 12, 24, 25, 24, 62, 62, 1, 8, 10, 10, 15, 15, 42, 42, 42, 42, 42, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 12, 12, 24, 62, 62, 62, 62, 62, 1, 1, 15, 15, 42] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 289 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478639 none CN(CC1CCN(C(=O)CNC(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 38, 42, 42, 42, 42, 59, 59, 127, 148, 148, 148, 201, 201, 42, 32, 36, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 38, 38, 42, 42, 42, 42, 42, 127, 127, 148, 201, 201, 201, 201, 201, 42, 42, 32, 32, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 793 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478639 none CN(CC1CCN(C(=O)CNC(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 88, 62, 62, 62, 62, 48, 28, 49, 10, 10, 1, 10, 1, 1, 1, 62, 126, 151, 151, 160, 160, 201, 201, 201, 201, 201, 126, 126, 126, 88, 88, 62, 62, 62, 62, 62, 28, 28, 10, 1, 1, 1, 1, 1, 62, 62, 160, 160, 201] 201 rigid atoms, others: [43, 40, 41, 42, 11, 44, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 689 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478639 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478639 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478639/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478639 Building REAL300025478640 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478640' /scratch/stefan/7787258/working/building/REAL300025478640 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478640 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478640/0 /scratch/stefan/7787258/working/building/REAL300025478640 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/526 `/scratch/stefan/7787258/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478640 none COCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 10, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 20, 32, 79, 79, 79, 79, 79, 1, 18, 18, 18, 16, 15, 13, 13, 12, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 20, 20, 79, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 262 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478640 none COCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 174, 89, 79, 89, 79, 79, 79, 70, 50, 37, 50, 25, 37, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 195, 195, 176, 176, 174, 174, 79, 79, 79, 79, 79, 70, 70, 50, 50, 50, 25, 25, 1, 79, 79] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 919 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478640 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478640 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478640/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478640 Building REAL300025478641 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478641' /scratch/stefan/7787258/working/building/REAL300025478641 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478641 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478641/0 /scratch/stefan/7787258/working/building/REAL300025478641 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/527 `/scratch/stefan/7787258/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)COC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478641 none CN(CC1CCN(C(=O)COC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 22, 32, 32, 32, 32, 1, 8, 12, 12, 13, 13, 35, 35, 35, 35, 35, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 13, 13, 35] 141 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 167 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: REAL300025478641 none CN(CC1CCN(C(=O)COC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [30, 29, 30, 32, 35, 35, 35, 35, 47, 47, 83, 115, 141, 141, 141, 141, 35, 26, 29, 13, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 32, 32, 35, 35, 35, 35, 35, 83, 83, 141, 141, 141, 141, 141, 141, 141, 141, 141, 35, 35, 26, 26, 1] 141 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 511 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: REAL300025478641 none CN(CC1CCN(C(=O)COC2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [72, 51, 32, 32, 32, 32, 25, 14, 25, 4, 1, 1, 1, 1, 1, 1, 32, 72, 94, 94, 100, 100, 141, 141, 141, 141, 141, 72, 72, 72, 51, 51, 32, 32, 32, 32, 32, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 100, 100, 141] 141 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 460 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478641 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478641 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478641/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478641 Building REAL300025478642 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478642' /scratch/stefan/7787258/working/building/REAL300025478642 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478642 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478642/0 /scratch/stefan/7787258/working/building/REAL300025478642 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/528 `/scratch/stefan/7787258/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478642 none CC1=NC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 23, 37, 37, 54, 54, 78, 120, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 23, 23, 37, 37, 37, 78, 78, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 554 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478642 none CC1=NC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 201, 201, 133, 105, 133, 105, 105, 105, 91, 67, 53, 67, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 133, 201, 105, 105, 105, 105, 105, 91, 91, 67, 67, 67, 29, 29, 1, 105, 105] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 851 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478642 none CC1=NC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 28, 43, 105, 105, 105, 105, 105, 1, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 105, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 9, 10, 11, 12, 13, 46, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 253 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478642 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478642 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478642/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478642 Building REAL300025478643 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478643' /scratch/stefan/7787258/working/building/REAL300025478643 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478643 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478643/0 /scratch/stefan/7787258/working/building/REAL300025478643 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/529 `/scratch/stefan/7787258/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478643 none CCSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 25, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 19, 28, 96, 96, 96, 96, 96, 1, 33, 33, 33, 32, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 19, 19, 96, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 279 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478643 none CCSCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 121, 121, 105, 96, 105, 96, 96, 96, 80, 48, 37, 48, 26, 37, 11, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 121, 121, 121, 121, 96, 96, 96, 96, 96, 80, 80, 48, 48, 48, 26, 26, 1, 96, 96] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 626 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478643 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478643 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478643/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478643 Building REAL300025478644 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478644' /scratch/stefan/7787258/working/building/REAL300025478644 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478644 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478644/0 /scratch/stefan/7787258/working/building/REAL300025478644 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/530 `/scratch/stefan/7787258/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478644 none CCOC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 13, 18, 18, 29, 29, 60, 101, 201, 201, 201, 201, 201, 6, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 18, 18, 18, 60, 60, 201, 6, 6] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 501 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478644 none CCOC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 178, 193, 178, 178, 178, 145, 95, 55, 95, 23, 55, 12, 1, 1, 1, 1, 1, 1, 1, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 178, 178, 145, 145, 95, 95, 95, 23, 23, 1, 178, 178] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 742 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478644 none CCOC1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 22, 22, 50, 86, 178, 178, 178, 178, 178, 1, 11, 11, 11, 11, 11, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 50, 50, 178, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 451 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478644 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478644 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478644/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478644 Building REAL300025478645 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478645' /scratch/stefan/7787258/working/building/REAL300025478645 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478645 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478645/0 /scratch/stefan/7787258/working/building/REAL300025478645 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/531 `/scratch/stefan/7787258/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NSN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478645 none CN(CC1CCN(C(=O)C2=NSN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 1, 13, 27, 27, 51, 79, 144, 144, 144, 144, 144, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 1, 1, 51, 51, 144] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 36, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 38, 39, 40]) total number of confs: 372 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478645 none CN(CC1CCN(C(=O)C2=NSN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 66, 73, 127, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 144, 37, 66, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 127, 127, 144, 144, 144, 144, 144, 201, 144, 144, 37, 37, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 819 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478645 none CN(CC1CCN(C(=O)C2=NSN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 6, 33, 58, 58, 99, 140, 201, 201, 201, 201, 201, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 1, 6, 6, 99, 99, 201] 201 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 576 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478645 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478645 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478645/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478645 Building REAL300025478646 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478646' /scratch/stefan/7787258/working/building/REAL300025478646 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478646 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478646/0 /scratch/stefan/7787258/working/building/REAL300025478646 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/532 `/scratch/stefan/7787258/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478646 none CN(CC1CCN(C(=O)C2=CN=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 1, 12, 23, 23, 40, 54, 94, 94, 94, 94, 94, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 40, 40, 94] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 36, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 38, 39, 40]) total number of confs: 258 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478646 none CN(CC1CCN(C(=O)C2=CN=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 54, 55, 82, 94, 94, 94, 94, 118, 118, 201, 201, 201, 201, 94, 36, 54, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 82, 82, 94, 94, 94, 94, 94, 201, 94, 94, 36, 36, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 640 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478646 none CN(CC1CCN(C(=O)C2=CN=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 37, 65, 65, 107, 134, 201, 201, 201, 201, 201, 37, 37, 37, 23, 23, 8, 8, 8, 8, 8, 1, 8, 8, 107, 107, 201] 201 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 612 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478646 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478646 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478646/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478646 Building REAL300025478647 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478647' /scratch/stefan/7787258/working/building/REAL300025478647 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478647 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478647/0 /scratch/stefan/7787258/working/building/REAL300025478647 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/533 `/scratch/stefan/7787258/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478647 none COC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 11, 13, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 26, 43, 125, 125, 125, 125, 125, 1, 13, 13, 13, 11, 5, 5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 26, 26, 125, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 305 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478647 none COC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 201, 176, 158, 125, 158, 125, 125, 125, 109, 71, 51, 71, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 176, 176, 176, 125, 125, 125, 125, 125, 109, 109, 71, 71, 71, 30, 30, 1, 125, 125] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 834 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478647 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478647 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478647/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478647 Building REAL300025478648 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478648' /scratch/stefan/7787258/working/building/REAL300025478648 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478648 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478648/0 /scratch/stefan/7787258/working/building/REAL300025478648 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/534 `/scratch/stefan/7787258/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478648 none CN(CC1CCN(C(=O)C2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 1, 12, 27, 27, 48, 73, 148, 148, 148, 148, 148, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 7, 7, 1, 1, 48, 48, 148] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 360 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: REAL300025478648 none CN(CC1CCN(C(=O)C2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 80, 132, 148, 148, 148, 148, 200, 200, 201, 201, 201, 201, 148, 37, 68, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 132, 132, 148, 148, 148, 148, 148, 201, 201, 148, 148, 37, 37, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 809 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: REAL300025478648 none CN(CC1CCN(C(=O)C2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 30, 57, 57, 92, 134, 201, 201, 201, 201, 201, 30, 30, 30, 18, 18, 7, 7, 7, 7, 7, 1, 1, 7, 7, 92, 92, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 542 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478648 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478648 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478648/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478648 Building REAL300025478649 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478649' /scratch/stefan/7787258/working/building/REAL300025478649 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478649 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478649/0 /scratch/stefan/7787258/working/building/REAL300025478649 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/535 `/scratch/stefan/7787258/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478649 none CCCSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 69, 41, 14, 2, 1, 2, 1, 1, 1, 1, 1, 4, 8, 8, 10, 10, 15, 20, 41, 41, 41, 41, 41, 1, 76, 76, 76, 76, 76, 69, 69, 14, 14, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 15, 15, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 368 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: REAL300025478649 none CCCSCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 123, 44, 41, 44, 41, 41, 41, 39, 31, 25, 31, 16, 25, 12, 1, 1, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 123, 123, 41, 41, 41, 41, 41, 39, 39, 31, 31, 31, 16, 16, 1, 41, 41] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 743 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478649 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478649 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478649/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478649 Building REAL300025478650 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478650' /scratch/stefan/7787258/working/building/REAL300025478650 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478650 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478650/0 /scratch/stefan/7787258/working/building/REAL300025478650 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/536 `/scratch/stefan/7787258/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478650 none CC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 16, 26, 79, 79, 79, 79, 79, 1, 9, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 16, 16, 79, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 214 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: REAL300025478650 none CC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 9, 17, 17, 17, 17, 37, 54, 54, 54, 54, 76, 113, 201, 201, 201, 201, 201, 17, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 37, 37, 54, 54, 54, 76, 76, 201, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 562 number of broken/clashed sets: 95 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478650 none CC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 87, 79, 87, 79, 79, 79, 69, 54, 38, 54, 26, 38, 13, 1, 1, 1, 1, 1, 1, 1, 79, 147, 201, 201, 147, 147, 147, 147, 79, 79, 79, 79, 79, 69, 69, 54, 54, 54, 26, 26, 1, 79, 79, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 764 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478650 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478650 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478650/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478650 Building REAL300025478651 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478651' /scratch/stefan/7787258/working/building/REAL300025478651 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478651 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478651/0 /scratch/stefan/7787258/working/building/REAL300025478651 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/537 `/scratch/stefan/7787258/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478651 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 26, 36, 36, 47, 47, 80, 121, 201, 201, 201, 201, 201, 10, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 26, 26, 36, 36, 36, 80, 80, 201, 10, 10, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 561 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478651 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 122, 155, 122, 122, 122, 110, 75, 52, 75, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 110, 110, 75, 75, 75, 28, 28, 1, 122, 122, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 704 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478651 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 35, 57, 122, 122, 122, 122, 122, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 35, 35, 122, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 43, 5, 7, 8, 9, 10, 11, 44, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 296 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478651 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478651/1 /scratch/stefan/7787258/working/building/REAL300025478651 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/538 `/scratch/stefan/7787258/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1) `REAL300025478651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478651 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 19, 33, 33, 51, 51, 79, 118, 201, 201, 201, 201, 201, 7, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 7, 19, 19, 33, 33, 33, 79, 79, 201, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 534 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478651 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 164, 201, 164, 164, 164, 149, 107, 65, 107, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 149, 149, 107, 107, 107, 29, 29, 1, 164, 164, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 747 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478651 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 15, 15, 31, 31, 55, 87, 164, 164, 164, 164, 164, 1, 7, 7, 8, 8, 8, 7, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 55, 55, 164, 1, 1, 7] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 409 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478651 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478651 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478651/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478651/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478651 Building REAL300025478652 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478652' /scratch/stefan/7787258/working/building/REAL300025478652 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478652 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478652/0 /scratch/stefan/7787258/working/building/REAL300025478652 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/539 `/scratch/stefan/7787258/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478652 none CN(CC1CCN(C(=O)C2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 1, 12, 27, 27, 52, 75, 129, 129, 129, 129, 129, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 1, 1, 52, 52, 129] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 348 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478652 none CN(CC1CCN(C(=O)C2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 65, 72, 110, 129, 129, 129, 129, 151, 151, 201, 201, 201, 201, 129, 38, 65, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 110, 110, 129, 129, 129, 129, 129, 201, 201, 129, 129, 38, 38, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 716 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478652 none CN(CC1CCN(C(=O)C2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 10, 33, 61, 61, 107, 141, 201, 201, 201, 201, 201, 33, 33, 33, 22, 22, 10, 10, 10, 10, 10, 1, 1, 10, 10, 107, 107, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 605 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478652 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478652 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478652/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478652 Building REAL300025478653 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478653' /scratch/stefan/7787258/working/building/REAL300025478653 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478653 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478653/0 /scratch/stefan/7787258/working/building/REAL300025478653 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/540 `/scratch/stefan/7787258/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478653 none CC1=NN(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 22, 32, 32, 53, 53, 80, 121, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 22, 22, 32, 32, 32, 80, 80, 201, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 560 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478653 none CC1=NN(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 149, 116, 149, 116, 116, 116, 94, 62, 45, 62, 25, 45, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 94, 94, 62, 62, 62, 25, 25, 1, 116, 116, 201] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 679 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478653 none CC1=NN(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 38, 58, 116, 116, 116, 116, 116, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 38, 38, 116, 1, 1, 9] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 291 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478653 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478653 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478653/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478653 Building REAL300025478654 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478654' /scratch/stefan/7787258/working/building/REAL300025478654 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478654 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478654/0 /scratch/stefan/7787258/working/building/REAL300025478654 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/541 `/scratch/stefan/7787258/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1) `REAL300025478654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478654 none CC1=CN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 11, 11, 34, 47, 47, 54, 54, 80, 122, 201, 201, 201, 201, 201, 11, 1, 1, 2, 2, 2, 1, 5, 5, 11, 11, 11, 11, 11, 34, 34, 47, 47, 47, 80, 80, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 48, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 573 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478654 none CC1=CN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 151, 109, 151, 109, 109, 109, 95, 71, 55, 71, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 109, 109, 109, 95, 95, 71, 71, 71, 27, 27, 1, 109, 109, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 840 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478654 none CC1=CN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 32, 47, 109, 109, 109, 109, 109, 1, 11, 11, 11, 11, 11, 11, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 109, 1, 1, 11] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 286 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478654 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478654 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478654/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478654 Building REAL300025478655 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478655' /scratch/stefan/7787258/working/building/REAL300025478655 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478655 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478655/0 /scratch/stefan/7787258/working/building/REAL300025478655 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/542 `/scratch/stefan/7787258/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478655 none CC(C)COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 26, 10, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 20, 33, 122, 122, 122, 122, 122, 1, 26, 26, 26, 26, 26, 26, 26, 18, 18, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 20, 20, 122, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 336 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478655 none CC(C)COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 191, 162, 130, 162, 122, 130, 122, 122, 122, 92, 48, 44, 48, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 122, 122, 122, 122, 122, 92, 92, 48, 48, 48, 29, 29, 1, 122, 122] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 816 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478655 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478655 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478655/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478655 Building REAL300025478656 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478656' /scratch/stefan/7787258/working/building/REAL300025478656 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478656 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478656/0 /scratch/stefan/7787258/working/building/REAL300025478656 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/543 `/scratch/stefan/7787258/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478656 none CCCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 65, 19, 19, 19, 9, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 9, 9, 17, 23, 58, 58, 58, 58, 58, 1, 74, 74, 74, 74, 74, 65, 65, 19, 9, 9, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 17, 17, 58, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 50, 51, 41, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 466 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478656 none CCCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 138, 106, 60, 58, 60, 58, 58, 58, 56, 43, 30, 43, 16, 30, 12, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 138, 106, 106, 58, 58, 58, 58, 58, 56, 56, 43, 43, 43, 16, 16, 1, 58, 58] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 910 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478656 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478656 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478656/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478656 Building REAL300025478657 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478657' /scratch/stefan/7787258/working/building/REAL300025478657 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478657 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478657/0 /scratch/stefan/7787258/working/building/REAL300025478657 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/544 `/scratch/stefan/7787258/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478657 none CCC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 14, 14, 30, 44, 126, 126, 126, 126, 126, 1, 16, 16, 16, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 126, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 321 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478657 none CCC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 201, 126, 137, 126, 126, 126, 102, 78, 53, 78, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 126, 126, 126, 102, 102, 78, 78, 78, 30, 30, 1, 126, 126] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 759 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478657 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478657 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478657/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478657 Building REAL300025478658 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478658' /scratch/stefan/7787258/working/building/REAL300025478658 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478658 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478658/0 /scratch/stefan/7787258/working/building/REAL300025478658 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/545 `/scratch/stefan/7787258/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CS(C)(=O)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478658 none CN(CC1CCN(C(=O)CS(C)(=O)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 18, 33, 33, 33, 1, 10, 15, 15, 23, 25, 47, 47, 47, 47, 47, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 19, 18, 33, 33, 33, 1, 1, 23, 23, 47] 102 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 261 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478658 none CN(CC1CCN(C(=O)CS(C)(=O)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 38, 39, 44, 47, 47, 47, 47, 75, 75, 99, 102, 102, 102, 47, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 44, 44, 47, 47, 47, 47, 47, 99, 99, 102, 102, 102, 47, 47, 29, 29, 1] 102 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 418 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478658 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478658 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478658/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478658 Building REAL300025478659 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478659' /scratch/stefan/7787258/working/building/REAL300025478659 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478659 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478659/0 /scratch/stefan/7787258/working/building/REAL300025478659 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/546 `/scratch/stefan/7787258/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C=C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478659 none CN(CC1CCN(C(=O)C=C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 1, 13, 28, 28, 54, 69, 124, 124, 124, 124, 124, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 54, 54, 124] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 343 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: REAL300025478659 none CN(CC1CCN(C(=O)C=C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 68, 74, 106, 124, 124, 124, 124, 133, 133, 201, 201, 201, 201, 201, 201, 124, 34, 68, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 106, 106, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 34, 34, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 768 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: REAL300025478659 none CN(CC1CCN(C(=O)C=C2CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 35, 66, 66, 115, 144, 201, 201, 201, 201, 201, 35, 35, 35, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 115, 115, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 632 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478659 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478659 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478659/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478659 Building REAL300025478660 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478660' /scratch/stefan/7787258/working/building/REAL300025478660 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478660 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478660/0 /scratch/stefan/7787258/working/building/REAL300025478660 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/547 `/scratch/stefan/7787258/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1) `REAL300025478660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478660 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 23, 32, 32, 55, 55, 82, 124, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 23, 23, 32, 32, 32, 82, 82, 201, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 558 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: REAL300025478660 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 150, 104, 150, 104, 104, 104, 96, 66, 46, 66, 27, 46, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 96, 96, 66, 66, 66, 27, 27, 1, 104, 104, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 685 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: REAL300025478660 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 35, 53, 104, 104, 104, 104, 104, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 35, 35, 104, 1, 1, 9] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 272 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478660 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478660 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478660/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478660 Building REAL300025478661 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478661' /scratch/stefan/7787258/working/building/REAL300025478661 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478661 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478661/0 /scratch/stefan/7787258/working/building/REAL300025478661 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/548 `/scratch/stefan/7787258/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478661 none CCOC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 12, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 27, 42, 129, 129, 129, 129, 129, 1, 11, 11, 11, 11, 11, 9, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 27, 27, 129, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 317 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478661 none CCOC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 201, 201, 129, 141, 129, 129, 129, 113, 72, 52, 72, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 113, 113, 72, 72, 72, 30, 30, 1, 129, 129] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 892 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478661 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478661 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478661/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478661 Building REAL300025478662 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478662' /scratch/stefan/7787258/working/building/REAL300025478662 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478662 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478662/0 /scratch/stefan/7787258/working/building/REAL300025478662 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/549 `/scratch/stefan/7787258/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478662 none CN(CC1CCN(C(=O)CC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 15, 14, 1, 11, 26, 26, 48, 67, 133, 133, 133, 133, 133, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 15, 14, 1, 1, 48, 48, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 369 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478662 none CN(CC1CCN(C(=O)CC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 79, 86, 123, 133, 133, 133, 133, 135, 135, 201, 201, 201, 201, 133, 38, 79, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 123, 123, 133, 133, 133, 133, 133, 201, 201, 133, 133, 38, 38, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 898 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478662 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478662 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478662/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478662 Building REAL300025478663 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478663' /scratch/stefan/7787258/working/building/REAL300025478663 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478663 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478663/0 /scratch/stefan/7787258/working/building/REAL300025478663 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/550 `/scratch/stefan/7787258/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478663 none COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 35, 59, 153, 153, 153, 153, 153, 1, 11, 11, 11, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 35, 35, 153, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 359 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478663 none COC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 201, 153, 162, 153, 153, 153, 138, 100, 67, 100, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 138, 138, 100, 100, 100, 30, 30, 1, 153, 153] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 847 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478663 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478663 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478663/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478663 Building REAL300025478664 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478664' /scratch/stefan/7787258/working/building/REAL300025478664 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478664 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478664/0 /scratch/stefan/7787258/working/building/REAL300025478664 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/551 `/scratch/stefan/7787258/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478664 none CC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 15, 19, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 25, 40, 94, 94, 94, 94, 94, 1, 19, 19, 19, 19, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 25, 25, 94, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 275 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478664 none CC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 150, 121, 94, 121, 94, 94, 94, 80, 57, 43, 57, 25, 43, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 150, 150, 94, 94, 94, 94, 94, 80, 80, 57, 57, 57, 25, 25, 1, 94, 94] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 757 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478664 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478664 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478664/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478664 Building REAL300025478665 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478665' /scratch/stefan/7787258/working/building/REAL300025478665 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478665 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478665/0 /scratch/stefan/7787258/working/building/REAL300025478665 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/552 `/scratch/stefan/7787258/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CC1)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478665 none CC(OCC1CC1)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 1, 1, 1, 1, 25, 34, 34, 50, 50, 50, 50, 82, 94, 94, 108, 108, 134, 166, 201, 201, 201, 201, 201, 50, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 82, 82, 94, 94, 94, 134, 134, 201, 50, 50] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 35, 36, 37] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 671 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478665 none CC(OCC1CC1)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 72, 106, 120, 178, 201, 201, 69, 72, 69, 69, 69, 63, 48, 33, 48, 18, 33, 12, 1, 1, 1, 1, 1, 1, 1, 69, 106, 106, 106, 106, 178, 178, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 63, 63, 48, 48, 48, 18, 18, 1, 69, 69] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 903 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478665 none CC(OCC1CC1)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 9, 23, 50, 50, 1, 3, 1, 1, 1, 1, 1, 4, 8, 8, 11, 11, 21, 29, 69, 69, 69, 69, 69, 1, 5, 5, 5, 5, 23, 23, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 21, 21, 69, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 333 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478665 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478665 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478665/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478665 Building REAL300025478666 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478666' /scratch/stefan/7787258/working/building/REAL300025478666 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478666 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478666/0 /scratch/stefan/7787258/working/building/REAL300025478666 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/553 `/scratch/stefan/7787258/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478666 none CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 42, 23, 15, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 9, 9, 12, 15, 41, 41, 41, 41, 41, 1, 65, 65, 65, 65, 65, 42, 42, 15, 15, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 12, 12, 41, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478666 none CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 151, 44, 41, 44, 41, 41, 41, 40, 32, 29, 32, 16, 29, 12, 1, 1, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 151, 151, 41, 41, 41, 41, 41, 40, 40, 32, 32, 32, 16, 16, 1, 41, 41] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 789 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478666 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478666 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478666/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478666 Building REAL300025478667 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478667' /scratch/stefan/7787258/working/building/REAL300025478667 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478667 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478667/0 /scratch/stefan/7787258/working/building/REAL300025478667 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/554 `/scratch/stefan/7787258/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478667 none CCCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 18, 10, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 4, 7, 7, 11, 11, 22, 29, 53, 53, 53, 53, 53, 1, 32, 32, 32, 32, 32, 30, 30, 18, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 22, 22, 53, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 285 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478667 none CCCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 93, 86, 54, 86, 53, 54, 53, 53, 53, 46, 37, 27, 37, 16, 27, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 109, 109, 86, 86, 86, 86, 53, 53, 53, 53, 53, 46, 46, 37, 37, 37, 16, 16, 1, 53, 53] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 900 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478667 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478667 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478667/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478667 Building REAL300025478668 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478668' /scratch/stefan/7787258/working/building/REAL300025478668 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478668 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478668/0 /scratch/stefan/7787258/working/building/REAL300025478668 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/555 `/scratch/stefan/7787258/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478668 none C=CCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 35, 16, 8, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 4, 7, 7, 11, 11, 23, 31, 66, 66, 66, 66, 66, 1, 41, 41, 41, 35, 35, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 23, 23, 66, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 347 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478668 none C=CCCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 110, 102, 98, 68, 98, 66, 68, 66, 66, 66, 57, 46, 32, 46, 17, 32, 12, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 110, 110, 98, 98, 98, 98, 66, 66, 66, 66, 66, 57, 57, 46, 46, 46, 17, 17, 1, 66, 66] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 900 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478668 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478668 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478668/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478668 Building REAL300025478669 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478669' /scratch/stefan/7787258/working/building/REAL300025478669 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478669 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478669/0 /scratch/stefan/7787258/working/building/REAL300025478669 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/556 `/scratch/stefan/7787258/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478669 none CN(CC1CCN(C(=O)C2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 1, 14, 33, 33, 64, 85, 150, 150, 150, 150, 150, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 64, 64, 150] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478669 none CN(CC1CCN(C(=O)C2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 74, 91, 131, 150, 150, 150, 150, 166, 166, 201, 201, 201, 201, 150, 37, 74, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 131, 131, 150, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 37, 37, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 797 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478669 none CN(CC1CCN(C(=O)C2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 33, 63, 63, 109, 137, 201, 201, 201, 201, 201, 33, 33, 33, 18, 18, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 109, 109, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 600 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478669 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478669 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478669/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478669 Building REAL300025478670 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478670' /scratch/stefan/7787258/working/building/REAL300025478670 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478670 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478670/0 /scratch/stefan/7787258/working/building/REAL300025478670 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/557 `/scratch/stefan/7787258/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478670 none CN(CC1CCN(C(=O)C2=CC=NC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 1, 12, 28, 28, 53, 74, 123, 123, 123, 123, 123, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 53, 53, 123] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 340 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: REAL300025478670 none CN(CC1CCN(C(=O)C2=CC=NC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 67, 80, 112, 123, 123, 123, 123, 128, 128, 201, 201, 201, 201, 201, 201, 123, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 112, 112, 123, 123, 123, 123, 123, 201, 201, 201, 123, 123, 39, 39, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 645 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: REAL300025478670 none CN(CC1CCN(C(=O)C2=CC=NC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 28, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 45, 70, 70, 111, 142, 201, 201, 201, 201, 201, 45, 45, 45, 28, 28, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 111, 111, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 617 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478670 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478670 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478670/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478670 Building REAL300025478671 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478671' /scratch/stefan/7787258/working/building/REAL300025478671 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478671 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478671/0 /scratch/stefan/7787258/working/building/REAL300025478671 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/558 `/scratch/stefan/7787258/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1) `REAL300025478671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478671 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 25, 37, 37, 47, 47, 80, 115, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 9, 9, 9, 9, 9, 25, 25, 37, 37, 37, 80, 80, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 566 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478671 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 139, 156, 139, 139, 139, 118, 74, 50, 74, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 118, 118, 74, 74, 74, 28, 28, 1, 139, 139] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 690 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478671 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 44, 65, 139, 139, 139, 139, 139, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 44, 44, 139, 1, 1] 201 rigid atoms, others: [32, 33, 34, 43, 5, 7, 8, 9, 10, 11, 44, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478671 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478671 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478671/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478671 Building REAL300025478672 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478672' /scratch/stefan/7787258/working/building/REAL300025478672 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478672 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478672/0 /scratch/stefan/7787258/working/building/REAL300025478672 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/559 `/scratch/stefan/7787258/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478672 none CN(CC1CCN(C(=O)C2=CC=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 13, 26, 26, 53, 76, 126, 126, 126, 126, 126, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 53, 53, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 349 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: REAL300025478672 none CN(CC1CCN(C(=O)C2=CC=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 62, 75, 109, 126, 126, 126, 126, 168, 168, 201, 201, 201, 201, 201, 126, 33, 62, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 109, 109, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 126, 126, 33, 33, 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: 749 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: REAL300025478672 none CN(CC1CCN(C(=O)C2=CC=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 38, 64, 64, 108, 142, 201, 201, 201, 201, 201, 38, 38, 38, 23, 23, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 10, 10, 108, 108, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 604 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478672 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478672 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478672/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478672 Building REAL300025478673 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478673' /scratch/stefan/7787258/working/building/REAL300025478673 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478673 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478673/0 /scratch/stefan/7787258/working/building/REAL300025478673 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/560 `/scratch/stefan/7787258/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478673 none CCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 3, 9, 12, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 28, 46, 139, 139, 139, 139, 139, 1, 13, 13, 13, 13, 13, 9, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 139, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 341 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478673 none CCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 201, 154, 201, 201, 139, 154, 139, 139, 139, 117, 73, 53, 73, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 117, 117, 73, 73, 73, 28, 28, 1, 139, 139] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 890 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478673 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478673 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478673/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478673 Building REAL300025478674 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478674' /scratch/stefan/7787258/working/building/REAL300025478674 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478674 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478674/0 /scratch/stefan/7787258/working/building/REAL300025478674 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/561 `/scratch/stefan/7787258/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478674 none COCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 56, 29, 23, 15, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 18, 24, 51, 51, 51, 51, 51, 1, 69, 69, 69, 55, 55, 30, 30, 25, 25, 15, 15, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 18, 18, 51, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 425 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: REAL300025478674 none COCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 135, 130, 114, 55, 51, 55, 51, 51, 51, 41, 36, 29, 36, 16, 29, 13, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 135, 135, 132, 132, 114, 114, 51, 51, 51, 51, 51, 41, 41, 36, 36, 36, 16, 16, 1, 51, 51] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 901 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478674 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478674 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478674/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478674 Building REAL300025478675 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478675' /scratch/stefan/7787258/working/building/REAL300025478675 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478675 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478675/0 /scratch/stefan/7787258/working/building/REAL300025478675 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/562 `/scratch/stefan/7787258/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478675 none CCCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 20, 30, 70, 70, 70, 70, 70, 1, 35, 35, 35, 35, 35, 35, 35, 22, 22, 22, 22, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 20, 20, 70, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 307 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478675 none CCCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 170, 198, 77, 70, 77, 70, 70, 70, 62, 52, 35, 52, 18, 35, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 198, 170, 170, 70, 70, 70, 70, 70, 62, 62, 52, 52, 52, 18, 18, 1, 70, 70] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 826 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478675 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478675 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478675/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478675 Building REAL300025478676 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478676' /scratch/stefan/7787258/working/building/REAL300025478676 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478676 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478676/0 /scratch/stefan/7787258/working/building/REAL300025478676 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/563 `/scratch/stefan/7787258/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478676 none COC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 9, 16, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 27, 39, 103, 103, 103, 103, 103, 1, 20, 20, 20, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 27, 27, 103, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 302 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478676 none COC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 201, 125, 103, 125, 103, 103, 103, 88, 63, 46, 63, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 197, 197, 103, 103, 103, 103, 103, 88, 88, 63, 63, 63, 30, 30, 1, 103, 103] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 871 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478676 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478676 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478676/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478676 Building REAL300025478677 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478677' /scratch/stefan/7787258/working/building/REAL300025478677 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478677 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478677/0 /scratch/stefan/7787258/working/building/REAL300025478677 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/564 `/scratch/stefan/7787258/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478677 none CN(CC1CCN(C(=O)CC2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 14, 33, 33, 33, 33, 33, 1, 8, 10, 10, 12, 12, 27, 27, 27, 27, 27, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 14, 14, 33, 33, 33, 33, 33, 1, 1, 12, 12, 27] 82 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478677 none CN(CC1CCN(C(=O)CC2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 27, 27, 27, 27, 28, 28, 59, 82, 82, 82, 82, 82, 27, 23, 25, 12, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 27, 27, 27, 27, 27, 59, 59, 82, 82, 82, 82, 82, 27, 27, 23, 23, 1] 82 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 261 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478677 none CN(CC1CCN(C(=O)CC2=CN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [53, 45, 33, 33, 33, 33, 24, 9, 24, 1, 1, 1, 1, 1, 1, 1, 33, 53, 57, 57, 67, 67, 82, 82, 82, 82, 82, 53, 53, 53, 45, 45, 33, 33, 33, 33, 33, 9, 9, 1, 2, 2, 2, 1, 33, 33, 67, 67, 82] 82 rigid atoms, others: [43, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 291 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478677 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478677 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478677/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478677 Building REAL300025478678 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478678' /scratch/stefan/7787258/working/building/REAL300025478678 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478678 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478678/0 /scratch/stefan/7787258/working/building/REAL300025478678 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/565 `/scratch/stefan/7787258/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478678 none CN(CC1CCN(C(=O)C2CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 12, 30, 30, 59, 78, 128, 128, 128, 128, 128, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 59, 59, 128] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 371 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478678 none CN(CC1CCN(C(=O)C2CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 61, 78, 112, 128, 128, 128, 128, 135, 135, 201, 201, 201, 201, 201, 201, 128, 36, 61, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 112, 112, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 36, 36, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 816 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478678 none CN(CC1CCN(C(=O)C2CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 30, 60, 60, 107, 137, 201, 201, 201, 201, 201, 30, 30, 30, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 50, 51, 52, 53, 54]) total number of confs: 609 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478678 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478678 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478678/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478678 Building REAL300025478679 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478679' /scratch/stefan/7787258/working/building/REAL300025478679 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478679 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478679/0 /scratch/stefan/7787258/working/building/REAL300025478679 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/566 `/scratch/stefan/7787258/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478679 none C=CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 25, 41, 124, 124, 124, 124, 124, 1, 19, 19, 19, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 124, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 316 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478679 none C=CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 124, 136, 124, 124, 124, 105, 65, 48, 65, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 124, 105, 105, 65, 65, 65, 29, 29, 1, 124, 124] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 836 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478679 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478679 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478679/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478679 Building REAL300025478680 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478680' /scratch/stefan/7787258/working/building/REAL300025478680 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478680 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478680/0 /scratch/stefan/7787258/working/building/REAL300025478680 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/567 `/scratch/stefan/7787258/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=COCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478680 none CN(CC1CCN(C(=O)C2=COCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 14, 29, 29, 57, 78, 148, 148, 148, 148, 148, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 57, 57, 148] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 393 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478680 none CN(CC1CCN(C(=O)C2=COCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 74, 86, 130, 148, 148, 148, 148, 161, 161, 201, 201, 201, 201, 201, 148, 38, 74, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 130, 130, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 148, 148, 38, 38, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 733 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478680 none CN(CC1CCN(C(=O)C2=COCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 21, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 36, 62, 62, 108, 138, 201, 201, 201, 201, 201, 36, 36, 36, 21, 21, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 108, 108, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 605 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478680 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478680 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478680/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478680 Building REAL300025478681 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478681' /scratch/stefan/7787258/working/building/REAL300025478681 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478681 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478681/0 /scratch/stefan/7787258/working/building/REAL300025478681 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/568 `/scratch/stefan/7787258/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478681 none COC(=O)C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 19, 28, 28, 40, 40, 70, 108, 191, 191, 191, 191, 191, 8, 3, 3, 3, 1, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 28, 28, 28, 70, 70, 191, 8, 8] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 511 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478681 none COC(=O)C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 201, 191, 191, 138, 128, 138, 128, 128, 128, 119, 87, 64, 87, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 191, 191, 191, 191, 128, 128, 128, 128, 128, 119, 119, 87, 87, 87, 30, 30, 1, 128, 128] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 747 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478681 none COC(=O)C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 41, 66, 128, 128, 128, 128, 128, 1, 10, 10, 10, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 41, 41, 128, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 342 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478681 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478681 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478681/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478681 Building REAL300025478682 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478682' /scratch/stefan/7787258/working/building/REAL300025478682 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478682 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478682/0 /scratch/stefan/7787258/working/building/REAL300025478682 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/569 `/scratch/stefan/7787258/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478682 none CN(CC1CCN(C(=O)C2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 13, 30, 30, 66, 91, 156, 156, 156, 156, 156, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 66, 66, 156] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 435 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478682 none CN(CC1CCN(C(=O)C2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 71, 91, 133, 156, 156, 156, 156, 178, 178, 201, 201, 201, 201, 201, 156, 36, 71, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 133, 133, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 36, 36, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 805 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478682 none CN(CC1CCN(C(=O)C2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 31, 59, 59, 108, 137, 201, 201, 201, 201, 201, 31, 31, 31, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 108, 108, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 600 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478682 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478682 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478682/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478682 Building REAL300025478683 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478683' /scratch/stefan/7787258/working/building/REAL300025478683 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478683 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478683/0 /scratch/stefan/7787258/working/building/REAL300025478683 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/570 `/scratch/stefan/7787258/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478683 none CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 30, 48, 137, 137, 137, 137, 137, 1, 15, 15, 15, 14, 14, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 137, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 328 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478683 none CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 200, 174, 137, 174, 137, 137, 137, 119, 75, 54, 75, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 200, 200, 200, 200, 137, 137, 137, 137, 137, 119, 119, 75, 75, 75, 29, 29, 1, 137, 137] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 837 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478683 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478683 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478683/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478683 Building REAL300025478684 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478684' /scratch/stefan/7787258/working/building/REAL300025478684 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478684 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478684/0 /scratch/stefan/7787258/working/building/REAL300025478684 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/571 `/scratch/stefan/7787258/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478684 none CCNC(=O)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 24, 24, 15, 24, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 15, 15, 20, 25, 54, 54, 54, 54, 54, 1, 50, 50, 50, 50, 50, 24, 15, 15, 12, 12, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 20, 20, 54, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 50, 51, 41, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 352 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478684 none CCNC(=O)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 130, 133, 129, 68, 54, 68, 54, 54, 54, 43, 38, 31, 38, 17, 31, 12, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 133, 130, 130, 129, 129, 54, 54, 54, 54, 54, 43, 43, 38, 38, 38, 17, 17, 1, 54, 54] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 931 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478684 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478684 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478684/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478684 Building REAL300025478685 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478685' /scratch/stefan/7787258/working/building/REAL300025478685 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478685 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478685/0 /scratch/stefan/7787258/working/building/REAL300025478685 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/572 `/scratch/stefan/7787258/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478685 none CN(CC1CCN(C(=O)C2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 1, 13, 32, 32, 57, 83, 154, 154, 154, 154, 154, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 1, 57, 57, 154] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 389 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478685 none CN(CC1CCN(C(=O)C2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 68, 78, 138, 154, 154, 154, 154, 201, 201, 201, 201, 201, 201, 154, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 138, 138, 154, 154, 154, 154, 154, 201, 201, 154, 154, 36, 36, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 828 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478685 none CN(CC1CCN(C(=O)C2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 5, 27, 58, 58, 96, 135, 201, 201, 201, 201, 201, 27, 27, 27, 14, 14, 5, 5, 5, 5, 5, 1, 1, 5, 5, 96, 96, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 556 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478685 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478685 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478685/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478685 Building REAL300025478686 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478686' /scratch/stefan/7787258/working/building/REAL300025478686 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478686 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478686/0 /scratch/stefan/7787258/working/building/REAL300025478686 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/573 `/scratch/stefan/7787258/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478686 none COCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 32, 52, 125, 125, 125, 125, 125, 1, 12, 12, 12, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 125, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 327 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478686 none COCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 201, 125, 170, 125, 125, 125, 103, 63, 49, 63, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 103, 103, 63, 63, 63, 28, 28, 1, 125, 125] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 842 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478686 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478686 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478686/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478686 Building REAL300025478687 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478687' /scratch/stefan/7787258/working/building/REAL300025478687 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478687 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478687/0 /scratch/stefan/7787258/working/building/REAL300025478687 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/574 `/scratch/stefan/7787258/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478687 none CN(CC1CCN(C(=O)CCCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 25, 27, 27, 25, 27, 1, 8, 12, 12, 17, 17, 41, 41, 41, 41, 41, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 17, 17, 41] 121 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 35, 52, 53, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478687 none CN(CC1CCN(C(=O)CCCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 34, 37, 41, 41, 41, 41, 51, 51, 112, 119, 121, 121, 119, 121, 41, 28, 33, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 37, 37, 41, 41, 41, 41, 41, 112, 112, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 41, 41, 28, 28, 1] 121 rigid atoms, others: [56, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 529 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478687 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478687 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478687/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478687 Building REAL300025478688 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478688' /scratch/stefan/7787258/working/building/REAL300025478688 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478688 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478688/0 /scratch/stefan/7787258/working/building/REAL300025478688 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/575 `/scratch/stefan/7787258/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478688 none C=CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 30, 18, 2, 1, 2, 1, 1, 1, 1, 1, 4, 8, 8, 10, 10, 15, 18, 45, 45, 45, 45, 45, 1, 59, 59, 59, 48, 48, 18, 18, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 15, 15, 45, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 325 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478688 none C=CCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 155, 48, 45, 48, 45, 45, 45, 43, 34, 28, 34, 16, 28, 12, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 155, 155, 45, 45, 45, 45, 45, 43, 43, 34, 34, 34, 16, 16, 1, 45, 45] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 810 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478688 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478688 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478688/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478688 Building REAL300025478689 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478689' /scratch/stefan/7787258/working/building/REAL300025478689 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478689 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478689/0 /scratch/stefan/7787258/working/building/REAL300025478689 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/576 `/scratch/stefan/7787258/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=COC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478689 none CN(CC1CCN(C(=O)C2=COC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 1, 12, 29, 29, 51, 81, 156, 156, 156, 156, 156, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 6, 5, 1, 1, 51, 51, 156] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 383 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478689 none CN(CC1CCN(C(=O)C2=COC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 75, 82, 133, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 156, 39, 75, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 133, 133, 156, 156, 156, 156, 156, 201, 201, 156, 156, 39, 39, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 807 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478689 none CN(CC1CCN(C(=O)C2=COC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 23, 53, 53, 88, 126, 201, 201, 201, 201, 201, 23, 23, 23, 15, 15, 6, 6, 6, 6, 6, 1, 1, 5, 5, 88, 88, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 535 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478689 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478689 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478689/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478689 Building REAL300025478690 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478690' /scratch/stefan/7787258/working/building/REAL300025478690 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478690 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478690/0 /scratch/stefan/7787258/working/building/REAL300025478690 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/577 `/scratch/stefan/7787258/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478690 none CN(CC1CCN(C(=O)[C@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 1, 15, 34, 34, 72, 99, 171, 171, 171, 171, 171, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 72, 72, 171] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 463 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: REAL300025478690 none CN(CC1CCN(C(=O)[C@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 90, 108, 153, 171, 171, 171, 171, 191, 191, 201, 201, 201, 201, 201, 201, 171, 42, 90, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 153, 153, 171, 171, 171, 171, 171, 201, 201, 201, 201, 201, 171, 171, 42, 42, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 788 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: REAL300025478690 none CN(CC1CCN(C(=O)[C@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 35, 64, 64, 104, 132, 201, 201, 201, 201, 201, 35, 35, 35, 20, 20, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 104, 104, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46]) total number of confs: 559 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478690 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478690 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478690/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478690 Building REAL300025478691 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478691' /scratch/stefan/7787258/working/building/REAL300025478691 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478691 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478691/0 /scratch/stefan/7787258/working/building/REAL300025478691 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/578 `/scratch/stefan/7787258/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478691 none CN(CC1CCN(C(=O)CC2=CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 25, 25, 25, 25, 25, 1, 8, 10, 10, 12, 12, 31, 31, 31, 31, 31, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 12, 12, 31] 74 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478691 none CN(CC1CCN(C(=O)CC2=CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 27, 31, 31, 31, 31, 33, 33, 72, 74, 74, 74, 74, 74, 31, 22, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 27, 27, 31, 31, 31, 31, 31, 72, 72, 74, 74, 74, 74, 74, 74, 74, 74, 74, 31, 31, 22, 22, 1] 74 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478691 none CN(CC1CCN(C(=O)CC2=CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [48, 36, 25, 25, 25, 25, 16, 6, 16, 1, 1, 1, 1, 1, 1, 1, 25, 48, 56, 56, 60, 60, 74, 74, 74, 74, 74, 48, 48, 48, 36, 36, 25, 25, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 60, 60, 74] 74 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478691 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478691 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478691/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478691 Building REAL300025478692 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478692' /scratch/stefan/7787258/working/building/REAL300025478692 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478692 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478692/0 /scratch/stefan/7787258/working/building/REAL300025478692 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/579 `/scratch/stefan/7787258/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1) `REAL300025478692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478692 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 18, 29, 29, 49, 49, 74, 119, 201, 201, 201, 201, 201, 6, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 18, 18, 29, 29, 29, 74, 74, 201, 6, 6, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 529 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: REAL300025478692 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 178, 201, 178, 178, 178, 156, 105, 61, 105, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 178, 201, 201, 201, 201, 201, 178, 178, 178, 178, 178, 156, 156, 105, 105, 105, 28, 28, 1, 178, 178, 201, 201] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 768 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: REAL300025478692 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 14, 14, 33, 33, 55, 91, 178, 178, 178, 178, 178, 1, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 55, 55, 178, 1, 1, 6, 7] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 43, 42, 23, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 429 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478692 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478692/1 /scratch/stefan/7787258/working/building/REAL300025478692 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/580 `/scratch/stefan/7787258/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1) `REAL300025478692.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478692 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 26, 36, 36, 45, 45, 72, 110, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 1, 12, 12, 12, 12, 12, 26, 26, 36, 36, 36, 72, 72, 201, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 528 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478692 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 167, 125, 167, 125, 125, 125, 114, 86, 62, 86, 27, 62, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 114, 114, 86, 86, 86, 27, 27, 1, 125, 125, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 692 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478692 none CC1=NC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 33, 56, 125, 125, 125, 125, 125, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 33, 33, 125, 1, 1, 12] 201 rigid atoms, others: [32, 33, 34, 43, 5, 7, 8, 9, 10, 11, 44, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 302 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478692 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478692 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478692/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478692/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478692 Building REAL300025478693 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478693' /scratch/stefan/7787258/working/building/REAL300025478693 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478693 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478693/0 /scratch/stefan/7787258/working/building/REAL300025478693 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/581 `/scratch/stefan/7787258/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478693 none CSCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 10, 10, 23, 39, 100, 100, 100, 100, 100, 1, 14, 14, 14, 8, 8, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 100, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 252 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478693 none CSCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 165, 122, 165, 100, 122, 100, 100, 100, 85, 58, 42, 58, 27, 42, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 167, 167, 165, 165, 165, 165, 100, 100, 100, 100, 100, 85, 85, 58, 58, 58, 27, 27, 1, 100, 100] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 804 number of broken/clashed sets: 136 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478693 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478693 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478693/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478693 Building REAL300025478694 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478694' /scratch/stefan/7787258/working/building/REAL300025478694 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478694 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478694/0 /scratch/stefan/7787258/working/building/REAL300025478694 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/582 `/scratch/stefan/7787258/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 1, 6, 7, 7, 9, 9, 13, 13, 13, 13, 13, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 9, 13] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 53 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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 11, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 1] 13 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 26 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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 10, 10, 13, 13, 13, 13, 13, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 13] 13 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478694 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478694/1 /scratch/stefan/7787258/working/building/REAL300025478694 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/583 `/scratch/stefan/7787258/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478694.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 3, 5, 5, 7, 7, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 7, 7, 8] 8 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 34 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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1] 8 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 17 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: REAL300025478694 none CN(CC1CCN(C(=O)C2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 5, 5, 7, 7, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 8] 8 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 37 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478694 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478694 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478694/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478694/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478694 Building REAL300025478695 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478695' /scratch/stefan/7787258/working/building/REAL300025478695 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478695 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478695/0 /scratch/stefan/7787258/working/building/REAL300025478695 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/584 `/scratch/stefan/7787258/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478695 none CCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 12, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 10, 10, 27, 37, 91, 91, 91, 91, 91, 1, 59, 59, 59, 59, 59, 22, 12, 12, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 27, 27, 91, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 434 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478695 none CCC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 153, 153, 144, 92, 91, 92, 91, 91, 91, 84, 63, 39, 63, 19, 39, 12, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 153, 144, 144, 91, 91, 91, 91, 91, 84, 84, 63, 63, 63, 19, 19, 1, 91, 91] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 908 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478695 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478695 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478695/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478695 Building REAL300025478696 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478696' /scratch/stefan/7787258/working/building/REAL300025478696 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478696 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478696/0 /scratch/stefan/7787258/working/building/REAL300025478696 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/585 `/scratch/stefan/7787258/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C=CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478696 none CN(CC1CCN(C(=O)C=CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 6, 6, 6, 1, 5, 6, 6, 7, 7, 12, 12, 12, 12, 12, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 6, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 7, 7, 12] 14 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 51 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478696 none CN(CC1CCN(C(=O)C=CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 11, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 12, 10, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 10, 10, 1] 14 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 36 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478696 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478696 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478696/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478696 Building REAL300025478697 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478697' /scratch/stefan/7787258/working/building/REAL300025478697 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478697 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478697/0 /scratch/stefan/7787258/working/building/REAL300025478697 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/586 `/scratch/stefan/7787258/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(F)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478697 none CN(CC1CCN(C(=O)C2=CC=C(F)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 1, 14, 31, 31, 57, 88, 152, 152, 152, 152, 152, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 57, 57, 152] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 394 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: REAL300025478697 none CN(CC1CCN(C(=O)C2=CC=C(F)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 83, 98, 140, 152, 152, 152, 152, 165, 165, 201, 201, 201, 201, 201, 201, 152, 40, 83, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 140, 140, 152, 152, 152, 152, 152, 201, 201, 201, 152, 152, 40, 40, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 723 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: REAL300025478697 none CN(CC1CCN(C(=O)C2=CC=C(F)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 29, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 45, 74, 74, 110, 148, 201, 201, 201, 201, 201, 45, 45, 45, 29, 29, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 110, 110, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 600 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478697 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478697 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478697/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478697 Building REAL300025478698 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478698' /scratch/stefan/7787258/working/building/REAL300025478698 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478698 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478698/0 /scratch/stefan/7787258/working/building/REAL300025478698 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/587 `/scratch/stefan/7787258/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478698 none CC(C#N)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 9, 1, 4, 1, 1, 1, 1, 1, 5, 16, 16, 29, 29, 57, 80, 145, 145, 145, 145, 145, 1, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 57, 57, 145, 1, 1] 181 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 42, 41, 23, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 396 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478698 none CC(C#N)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 150, 181, 181, 145, 150, 145, 145, 145, 131, 96, 87, 96, 35, 87, 13, 1, 1, 1, 1, 1, 1, 1, 145, 181, 181, 181, 181, 145, 145, 145, 145, 145, 131, 131, 96, 96, 96, 35, 35, 1, 145, 145] 181 rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 757 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478698 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478698 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478698/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478698 Building REAL300025478699 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478699' /scratch/stefan/7787258/working/building/REAL300025478699 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478699 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478699/0 /scratch/stefan/7787258/working/building/REAL300025478699 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/588 `/scratch/stefan/7787258/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478699 none COCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 51, 50, 36, 18, 2, 1, 2, 1, 1, 1, 1, 1, 4, 8, 8, 11, 11, 20, 29, 51, 51, 51, 51, 51, 1, 56, 56, 56, 51, 51, 50, 50, 18, 18, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 20, 20, 51, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478699 none COCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 147, 54, 51, 54, 51, 51, 51, 49, 40, 30, 40, 16, 30, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 201, 201, 147, 147, 51, 51, 51, 51, 51, 49, 49, 40, 40, 40, 16, 16, 1, 51, 51] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 642 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478699 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478699 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478699/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478699 Building REAL300025478700 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478700' /scratch/stefan/7787258/working/building/REAL300025478700 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478700 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478700/0 /scratch/stefan/7787258/working/building/REAL300025478700 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/589 `/scratch/stefan/7787258/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478700 none CCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 31, 50, 153, 153, 153, 153, 153, 1, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 31, 31, 153, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 355 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478700 none CCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 168, 201, 153, 168, 153, 153, 153, 142, 107, 69, 107, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 142, 142, 107, 107, 107, 31, 31, 1, 153, 153] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 824 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478700 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478700 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478700/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478700 Building REAL300025478701 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478701' /scratch/stefan/7787258/working/building/REAL300025478701 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478701 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478701/0 /scratch/stefan/7787258/working/building/REAL300025478701 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/590 `/scratch/stefan/7787258/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478701 none CC1=NN(C)C=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 27, 38, 38, 51, 51, 77, 119, 201, 201, 201, 201, 201, 11, 2, 2, 2, 2, 2, 2, 1, 11, 11, 11, 11, 11, 27, 27, 38, 38, 38, 77, 77, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 553 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478701 none CC1=NN(C)C=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 160, 143, 160, 143, 143, 143, 122, 92, 66, 92, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 122, 122, 92, 92, 92, 29, 29, 1, 143, 143] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 678 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478701 none CC1=NN(C)C=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 21, 21, 40, 65, 143, 143, 143, 143, 143, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 40, 40, 143, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 345 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478701 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478701 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478701/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478701 Building REAL300025478702 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478702' /scratch/stefan/7787258/working/building/REAL300025478702 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478702 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478702/0 /scratch/stefan/7787258/working/building/REAL300025478702 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/591 `/scratch/stefan/7787258/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478702 none CN(CC1CCN(C(=O)C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 1, 1, 1, 1, 1, 1, 4, 4, 9, 8, 12, 12, 12, 1, 6, 7, 7, 9, 9, 18, 18, 18, 18, 18, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 9, 9, 18] 33 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478702 none CN(CC1CCN(C(=O)C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 33, 33, 33, 33, 33, 18, 16, 18, 12, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 16, 16, 1] 33 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478702 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478702 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478702/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478702 Building REAL300025478703 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478703' /scratch/stefan/7787258/working/building/REAL300025478703 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478703 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478703/0 /scratch/stefan/7787258/working/building/REAL300025478703 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/592 `/scratch/stefan/7787258/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC3CCC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478703 none CN(CC1CCN(C(=O)C2CC3CCC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 1, 14, 37, 37, 82, 114, 175, 175, 175, 175, 175, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 82, 82, 175] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 497 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478703 none CN(CC1CCN(C(=O)C2CC3CCC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 74, 100, 147, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 42, 74, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 147, 147, 175, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 42, 42, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 812 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478703 none CN(CC1CCN(C(=O)C2CC3CCC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 24, 52, 52, 101, 137, 201, 201, 201, 201, 201, 24, 24, 24, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 101, 101, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 574 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478703 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478703 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478703/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478703 Building REAL300025478704 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478704' /scratch/stefan/7787258/working/building/REAL300025478704 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478704 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478704/0 /scratch/stefan/7787258/working/building/REAL300025478704 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/593 `/scratch/stefan/7787258/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1) `REAL300025478704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478704 none CC1=CC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 9, 9, 12, 12, 12, 12, 30, 41, 41, 46, 46, 74, 113, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 6, 6, 12, 12, 12, 12, 12, 30, 30, 41, 41, 41, 74, 74, 201, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478704 none CC1=CC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 140, 100, 140, 100, 100, 100, 88, 68, 50, 68, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 200, 200, 100, 100, 100, 100, 100, 88, 88, 68, 68, 68, 27, 27, 1, 100, 100] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 839 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478704 none CC1=CC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 28, 43, 100, 100, 100, 100, 100, 1, 12, 12, 12, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 100, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 266 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478704 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478704 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478704/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478704 Building REAL300025478705 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478705' /scratch/stefan/7787258/working/building/REAL300025478705 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478705 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478705/0 /scratch/stefan/7787258/working/building/REAL300025478705 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/594 `/scratch/stefan/7787258/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1) `REAL300025478705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478705 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 18, 23, 23, 24, 24, 45, 66, 146, 146, 146, 146, 146, 10, 1, 1, 6, 6, 6, 6, 6, 1, 10, 10, 10, 10, 10, 18, 18, 23, 23, 23, 45, 45, 146, 10, 10, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 374 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: REAL300025478705 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 146, 146, 104, 94, 104, 94, 94, 94, 79, 50, 44, 50, 28, 43, 13, 1, 1, 1, 1, 1, 1, 1, 94, 146, 146, 201, 201, 201, 201, 201, 146, 94, 94, 94, 94, 94, 79, 79, 50, 50, 50, 28, 28, 1, 94, 94, 146] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 804 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: REAL300025478705 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 17, 28, 94, 94, 94, 94, 94, 1, 10, 10, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 17, 17, 94, 1, 1, 10] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 258 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478705 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478705 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478705/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478705 Building REAL300025478706 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478706' /scratch/stefan/7787258/working/building/REAL300025478706 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478706 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478706/0 /scratch/stefan/7787258/working/building/REAL300025478706 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/595 `/scratch/stefan/7787258/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NC=CN=C2N)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478706 none CN(CC1CCN(C(=O)C2=NC=CN=C2N)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 1, 12, 30, 30, 61, 83, 138, 138, 138, 138, 138, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 61, 61, 138] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 385 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478706 none CN(CC1CCN(C(=O)C2=NC=CN=C2N)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 67, 85, 124, 138, 138, 138, 138, 168, 168, 201, 201, 201, 201, 201, 201, 138, 34, 67, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 124, 124, 138, 138, 138, 138, 138, 201, 201, 201, 201, 138, 138, 34, 34, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 727 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478706 none CN(CC1CCN(C(=O)C2=NC=CN=C2N)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 17, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 30, 60, 60, 110, 144, 201, 201, 201, 201, 201, 30, 30, 30, 17, 17, 7, 7, 7, 7, 7, 1, 1, 2, 2, 7, 7, 110, 110, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 606 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478706 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478706 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478706/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478706 Building REAL300025478707 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478707' /scratch/stefan/7787258/working/building/REAL300025478707 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478707 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478707/0 /scratch/stefan/7787258/working/building/REAL300025478707 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/596 `/scratch/stefan/7787258/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478707 none CN(CC1CCN(C(=O)CCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 19, 32, 32, 1, 8, 12, 12, 18, 18, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 21, 21, 32, 32, 32, 32, 32, 1, 1, 18, 18, 50] 137 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 242 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: REAL300025478707 none CN(CC1CCN(C(=O)CCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 41, 44, 50, 50, 50, 50, 64, 64, 123, 126, 137, 137, 50, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 44, 44, 50, 50, 50, 50, 50, 123, 123, 127, 127, 137, 137, 137, 137, 137, 50, 50, 33, 33, 1] 137 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 561 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: REAL300025478707 none CN(CC1CCN(C(=O)CCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [73, 53, 32, 32, 32, 32, 20, 6, 20, 3, 1, 1, 1, 1, 32, 73, 95, 95, 109, 109, 137, 137, 137, 137, 137, 73, 73, 73, 53, 53, 32, 32, 32, 32, 32, 6, 6, 3, 3, 1, 1, 1, 1, 1, 32, 32, 109, 109, 137] 137 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48]) total number of confs: 475 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478707 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478707 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478707/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478707 Building REAL300025478708 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478708' /scratch/stefan/7787258/working/building/REAL300025478708 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478708 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478708/0 /scratch/stefan/7787258/working/building/REAL300025478708 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/597 `/scratch/stefan/7787258/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1) `REAL300025478708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478708 none CC1=C(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 25, 34, 34, 54, 54, 84, 126, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 34, 34, 34, 84, 84, 201, 10, 10, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 577 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478708 none CC1=C(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 155, 115, 155, 115, 115, 115, 98, 74, 51, 74, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 115, 98, 98, 74, 74, 74, 27, 27, 1, 115, 115, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 673 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478708 none CC1=C(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 38, 59, 115, 115, 115, 115, 115, 1, 10, 10, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 38, 38, 115, 1, 1, 10] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 309 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478708 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478708 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478708/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478708 Building REAL300025478709 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478709' /scratch/stefan/7787258/working/building/REAL300025478709 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478709 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478709/0 /scratch/stefan/7787258/working/building/REAL300025478709 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/598 `/scratch/stefan/7787258/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478709 none CN(CC1CCN(C(=O)CC2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 15, 30, 30, 30, 30, 30, 1, 8, 12, 12, 16, 16, 38, 38, 38, 38, 38, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 16, 16, 38] 129 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478709 none CN(CC1CCN(C(=O)CC2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [31, 29, 31, 33, 38, 38, 38, 38, 45, 45, 108, 129, 129, 129, 129, 129, 38, 25, 29, 13, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 33, 33, 38, 38, 38, 38, 38, 108, 108, 129, 129, 129, 129, 129, 129, 129, 129, 129, 38, 38, 25, 25, 1] 129 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 516 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478709 none CN(CC1CCN(C(=O)CC2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [70, 53, 30, 30, 30, 30, 17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 30, 70, 89, 89, 100, 100, 129, 129, 129, 129, 129, 70, 70, 70, 53, 53, 30, 30, 30, 30, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 100, 100, 129] 129 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 452 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478709 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478709 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478709/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478709 Building REAL300025478710 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478710' /scratch/stefan/7787258/working/building/REAL300025478710 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478710 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478710/0 /scratch/stefan/7787258/working/building/REAL300025478710 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/599 `/scratch/stefan/7787258/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478710 none CCCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 37, 22, 16, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 8, 10, 24, 24, 24, 24, 24, 1, 72, 72, 72, 72, 72, 72, 72, 37, 37, 16, 16, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 8, 8, 24, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 374 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478710 none CCCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 108, 90, 83, 26, 24, 26, 24, 24, 24, 23, 20, 20, 20, 13, 20, 10, 1, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 201, 201, 108, 108, 83, 83, 24, 24, 24, 24, 24, 23, 23, 20, 20, 20, 13, 13, 1, 24, 24] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 887 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478710 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478710 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478710/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478710 Building REAL300025478711 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478711' /scratch/stefan/7787258/working/building/REAL300025478711 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478711 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478711/0 /scratch/stefan/7787258/working/building/REAL300025478711 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/600 `/scratch/stefan/7787258/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478711 none CN(CC1CCN(C(=O)CC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 28, 28, 28, 28, 1, 10, 16, 16, 25, 27, 55, 55, 55, 55, 55, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 18, 18, 28, 28, 1, 1, 25, 25, 55] 109 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478711 none CN(CC1CCN(C(=O)CC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [44, 42, 44, 49, 55, 55, 55, 55, 74, 74, 106, 109, 109, 109, 109, 55, 30, 42, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 49, 49, 55, 55, 55, 55, 55, 106, 106, 109, 109, 55, 55, 30, 30, 1] 109 rigid atoms, others: [44, 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]) total number of confs: 443 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478711 none CN(CC1CCN(C(=O)CC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [56, 43, 28, 28, 28, 28, 16, 5, 16, 1, 1, 1, 1, 1, 1, 28, 56, 68, 68, 83, 83, 109, 109, 109, 109, 109, 56, 56, 56, 43, 43, 28, 28, 28, 28, 28, 5, 5, 1, 1, 28, 28, 83, 83, 109] 109 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 349 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478711 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478711 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478711/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478711 Building REAL300025478712 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478712' /scratch/stefan/7787258/working/building/REAL300025478712 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478712 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478712/0 /scratch/stefan/7787258/working/building/REAL300025478712 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/601 `/scratch/stefan/7787258/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1) `REAL300025478712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478712 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 15, 23, 23, 30, 30, 64, 96, 189, 189, 189, 189, 189, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 15, 15, 23, 23, 23, 64, 64, 189, 5, 5, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 498 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478712 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 189, 169, 136, 169, 136, 136, 136, 121, 90, 62, 90, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 136, 189, 189, 189, 201, 201, 201, 201, 201, 136, 136, 136, 136, 136, 121, 121, 90, 90, 90, 28, 28, 1, 136, 136, 189] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 755 number of broken/clashed sets: 86 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478712 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 14, 14, 35, 56, 136, 136, 136, 136, 136, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 35, 35, 136, 1, 1, 5] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 339 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478712 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478712 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478712/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478712 Building REAL300025478713 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478713' /scratch/stefan/7787258/working/building/REAL300025478713 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478713 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478713/0 /scratch/stefan/7787258/working/building/REAL300025478713 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/602 `/scratch/stefan/7787258/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478713 none CN(CC1CCN(C(=O)CC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 15, 24, 24, 24, 24, 1, 8, 12, 12, 16, 16, 34, 34, 34, 34, 34, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 15, 15, 24, 24, 24, 24, 24, 24, 24, 1, 1, 16, 16, 34] 90 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 172 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: REAL300025478713 none CN(CC1CCN(C(=O)CC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 26, 28, 30, 34, 34, 34, 34, 40, 40, 84, 90, 90, 90, 90, 34, 22, 26, 12, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 30, 30, 34, 34, 34, 34, 34, 84, 84, 90, 90, 90, 90, 90, 90, 90, 34, 34, 22, 22, 1] 90 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 362 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: REAL300025478713 none CN(CC1CCN(C(=O)CC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 40, 24, 24, 24, 24, 15, 5, 15, 1, 1, 1, 1, 1, 1, 24, 53, 64, 64, 69, 69, 90, 90, 90, 90, 90, 53, 53, 53, 40, 40, 24, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 69, 69, 90] 90 rigid atoms, others: [43, 38, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 42] 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, 45, 46, 47, 48, 49]) total number of confs: 304 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478713 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478713 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478713/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478713 Building REAL300025478714 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478714' /scratch/stefan/7787258/working/building/REAL300025478714 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478714 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478714/0 /scratch/stefan/7787258/working/building/REAL300025478714 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/603 `/scratch/stefan/7787258/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478714 none CN(CC1CCN(C(=O)C2CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 1, 13, 29, 29, 57, 76, 134, 134, 134, 134, 134, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 57, 57, 134] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478714 none CN(CC1CCN(C(=O)C2CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 71, 86, 118, 134, 134, 134, 134, 141, 141, 201, 201, 201, 201, 134, 36, 71, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 118, 118, 134, 134, 134, 134, 134, 201, 201, 201, 201, 201, 201, 201, 134, 134, 36, 36, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 808 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478714 none CN(CC1CCN(C(=O)C2CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 19, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 32, 61, 61, 104, 136, 201, 201, 201, 201, 201, 32, 32, 32, 19, 19, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 104, 104, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478714 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478714 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478714/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478714 Building REAL300025478715 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478715' /scratch/stefan/7787258/working/building/REAL300025478715 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478715 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478715/0 /scratch/stefan/7787258/working/building/REAL300025478715 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/604 `/scratch/stefan/7787258/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478715 none CN(CC1CCN(C(=O)CC2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 38, 38, 38, 38, 1, 9, 14, 14, 22, 23, 47, 47, 47, 47, 47, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 22, 22, 38, 38, 38, 1, 1, 22, 22, 47] 139 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 217 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478715 none CN(CC1CCN(C(=O)CC2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 35, 37, 42, 47, 47, 47, 47, 75, 75, 136, 139, 139, 139, 139, 47, 29, 35, 12, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 42, 42, 47, 47, 47, 47, 47, 136, 136, 139, 139, 139, 47, 47, 29, 29, 1] 139 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: 571 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: REAL300025478715 none CN(CC1CCN(C(=O)CC2=NNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [76, 58, 38, 38, 38, 38, 21, 9, 21, 1, 1, 1, 1, 1, 1, 38, 76, 96, 96, 112, 112, 139, 139, 139, 139, 139, 76, 76, 76, 58, 58, 38, 38, 38, 38, 38, 9, 9, 1, 1, 1, 38, 38, 112, 112, 139] 139 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 461 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478715 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478715/1 /scratch/stefan/7787258/working/building/REAL300025478715 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/605 `/scratch/stefan/7787258/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478715.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478715 none CN(CC1CCN(C(=O)CC2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 20, 41, 41, 41, 41, 1, 10, 14, 14, 19, 19, 44, 44, 44, 44, 44, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 20, 20, 41, 41, 41, 1, 1, 19, 19, 44] 111 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478715 none CN(CC1CCN(C(=O)CC2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 38, 44, 44, 44, 44, 57, 57, 103, 111, 111, 111, 111, 44, 28, 35, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 38, 38, 44, 44, 44, 44, 44, 103, 103, 111, 111, 111, 44, 44, 28, 28, 1] 111 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: 438 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478715 none CN(CC1CCN(C(=O)CC2=CC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [68, 55, 41, 41, 41, 41, 28, 8, 28, 1, 1, 1, 1, 1, 1, 41, 68, 81, 81, 88, 88, 111, 111, 111, 111, 111, 68, 68, 68, 55, 55, 41, 41, 41, 41, 41, 8, 8, 1, 1, 1, 41, 41, 88, 88, 111] 111 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 348 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478715 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478715 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478715/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478715/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478715 Building REAL300025478716 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478716' /scratch/stefan/7787258/working/building/REAL300025478716 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478716 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478716/0 /scratch/stefan/7787258/working/building/REAL300025478716 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/606 `/scratch/stefan/7787258/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478716 none CN(CC1CCN(C(=O)C2=CC=NC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 1, 14, 30, 30, 60, 81, 142, 142, 142, 142, 142, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 60, 60, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 389 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478716 none CN(CC1CCN(C(=O)C2=CC=NC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 68, 83, 124, 142, 142, 142, 142, 151, 151, 201, 201, 201, 201, 201, 201, 142, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 124, 124, 142, 142, 142, 142, 142, 201, 201, 201, 142, 142, 36, 36, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 709 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478716 none CN(CC1CCN(C(=O)C2=CC=NC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 45, 70, 70, 111, 140, 201, 201, 201, 201, 201, 45, 45, 45, 27, 27, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 111, 111, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 614 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478716 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478716 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478716/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478716 Building REAL300025478717 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478717' /scratch/stefan/7787258/working/building/REAL300025478717 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478717 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478717/0 /scratch/stefan/7787258/working/building/REAL300025478717 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/607 `/scratch/stefan/7787258/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C) `REAL300025478717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478717 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 23, 29, 29, 53, 53, 81, 123, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 23, 23, 29, 29, 29, 81, 81, 201, 11, 11, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 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: REAL300025478717 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 111, 162, 111, 111, 111, 98, 71, 53, 71, 27, 53, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 98, 98, 71, 71, 71, 27, 27, 1, 111, 111, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 687 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: REAL300025478717 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 11, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 38, 60, 111, 111, 111, 111, 111, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 38, 38, 111, 1, 1, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 291 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478717 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478717 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478717/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478717 Building REAL300025478718 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478718' /scratch/stefan/7787258/working/building/REAL300025478718 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478718 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478718/0 /scratch/stefan/7787258/working/building/REAL300025478718 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/608 `/scratch/stefan/7787258/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478718 none CC1=CC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 21, 34, 34, 54, 54, 80, 120, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 34, 34, 34, 80, 80, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 557 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478718 none CC1=CC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 137, 157, 137, 137, 137, 115, 83, 60, 83, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 115, 115, 83, 83, 83, 29, 29, 1, 137, 137] 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, 46, 47]) total number of confs: 676 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478718 none CC1=CC=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 23, 23, 43, 65, 137, 137, 137, 137, 137, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 43, 43, 137, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478718 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478718 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478718/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478718 Building REAL300025478719 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478719' /scratch/stefan/7787258/working/building/REAL300025478719 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478719 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478719/0 /scratch/stefan/7787258/working/building/REAL300025478719 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/609 `/scratch/stefan/7787258/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478719 none CC1=CN=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 30, 41, 41, 47, 47, 72, 113, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 1, 1, 12, 12, 12, 12, 12, 30, 30, 41, 41, 41, 72, 72, 201, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 540 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478719 none CC1=CN=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 156, 142, 156, 142, 142, 142, 117, 85, 58, 85, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 117, 117, 85, 85, 85, 29, 29, 1, 142, 142, 201] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 676 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478719 none CC1=CN=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 38, 61, 142, 142, 142, 142, 142, 1, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 38, 38, 142, 1, 1, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 342 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478719 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478719 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478719/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478719 Building REAL300025478720 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478720' /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025478720 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478720/0 /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/610 `/scratch/stefan/7787258/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CN(C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478720 none CN(CC1CCN(C(=O)C2CN(C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 1, 13, 33, 33, 70, 99, 165, 165, 165, 165, 165, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 70, 70, 165] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 446 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: REAL300025478720 none CN(CC1CCN(C(=O)C2CN(C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 64, 88, 141, 165, 165, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 165, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 141, 141, 165, 165, 165, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 37, 37, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 821 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: REAL300025478720 none CN(CC1CCN(C(=O)C2CN(C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 10, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 24, 50, 50, 99, 136, 201, 201, 201, 201, 201, 24, 24, 24, 11, 11, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 99, 99, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 46, 39, 44] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 585 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478720/1 /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/611 `/scratch/stefan/7787258/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2C[N@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478720.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 3, 5, 5, 8, 9, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 8, 8, 10] 10 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 48, 17, 35, 36, 49, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 50 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: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 1] 10 rigid atoms, others: [52, 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, 19, 20, 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: 19 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: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 8, 8, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 10, 10, 10] 10 rigid atoms, others: [45, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 46, 39, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 48, 49, 50, 51, 52]) total number of confs: 39 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `2' /scratch/stefan/7787258/working/building/REAL300025478720/2 /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 2 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/612 `/scratch/stefan/7787258/working/3D/612' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2C[N@@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478720.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025478720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478720/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 1, 11, 15, 15, 25, 29, 39, 39, 39, 39, 39, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 25, 25, 39] 39 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 48, 17, 35, 36, 49, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 135 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: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 28, 12, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 1] 39 rigid atoms, others: [52, 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, 19, 20, 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: 138 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: REAL300025478720 none CN(CC1CCN(C(=O)C2C[N@@H+](C)CCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 20, 20, 30, 33, 39, 39, 39, 39, 39, 16, 16, 16, 10, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 39] 39 rigid atoms, others: [45, 43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478720 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478720 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478720/1.* 2: /scratch/stefan/7787258/working/building/REAL300025478720/2.* 0: /scratch/stefan/7787258/working/building/REAL300025478720/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478720 Building REAL300025478721 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478721' /scratch/stefan/7787258/working/building/REAL300025478721 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478721 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478721/0 /scratch/stefan/7787258/working/building/REAL300025478721 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/613 `/scratch/stefan/7787258/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478721 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 23, 35, 35, 52, 52, 84, 123, 201, 201, 201, 201, 201, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 23, 23, 35, 35, 35, 84, 84, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 576 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478721 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 144, 123, 144, 123, 123, 123, 112, 81, 52, 81, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 112, 112, 81, 81, 81, 28, 28, 1, 123, 123] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 658 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478721 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 41, 62, 123, 123, 123, 123, 123, 1, 8, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 41, 41, 123, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 329 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478721 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478721 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478721/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478721 Building REAL300025478722 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478722' /scratch/stefan/7787258/working/building/REAL300025478722 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478722 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478722/0 /scratch/stefan/7787258/working/building/REAL300025478722 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/614 `/scratch/stefan/7787258/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478722 none CN(CC1CCN(C(=O)CCC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 15, 22, 23, 22, 23, 1, 9, 14, 14, 21, 22, 44, 44, 44, 44, 44, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 16, 15, 22, 22, 1, 1, 21, 21, 44] 104 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478722 none CN(CC1CCN(C(=O)CCC(F)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [36, 34, 36, 39, 44, 44, 44, 44, 58, 58, 99, 104, 104, 104, 104, 44, 29, 34, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 39, 39, 44, 44, 44, 44, 44, 99, 99, 104, 104, 44, 44, 29, 29, 1] 104 rigid atoms, others: [44, 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]) total number of confs: 435 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478722 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478722 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478722/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478722 Building REAL300025478723 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478723' /scratch/stefan/7787258/working/building/REAL300025478723 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478723 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478723/0 /scratch/stefan/7787258/working/building/REAL300025478723 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/615 `/scratch/stefan/7787258/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478723 none C=CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 41, 20, 16, 11, 10, 2, 1, 2, 1, 1, 1, 1, 1, 5, 11, 11, 24, 24, 24, 28, 89, 89, 89, 89, 89, 1, 48, 48, 48, 41, 41, 16, 15, 12, 12, 10, 10, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 24, 24, 89, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478723 none C=CCOCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 184, 171, 163, 160, 109, 89, 109, 89, 89, 89, 71, 59, 44, 59, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 171, 170, 164, 164, 160, 160, 89, 89, 89, 89, 89, 71, 71, 59, 59, 59, 29, 29, 1, 89, 89] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 844 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478723 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478723 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478723/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478723 Building REAL300025478724 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478724' /scratch/stefan/7787258/working/building/REAL300025478724 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478724 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478724/0 /scratch/stefan/7787258/working/building/REAL300025478724 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/616 `/scratch/stefan/7787258/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478724 none CN(CC1CCN(C(=O)CC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 19, 29, 29, 29, 1, 8, 12, 12, 18, 19, 44, 44, 44, 44, 44, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 19, 19, 29, 29, 29, 29, 29, 29, 29, 1, 1, 18, 18, 44] 119 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478724 none CN(CC1CCN(C(=O)CC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 37, 39, 40, 44, 44, 44, 44, 53, 53, 98, 119, 119, 119, 44, 31, 37, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 40, 40, 44, 44, 44, 44, 44, 98, 98, 119, 119, 119, 119, 119, 119, 119, 44, 44, 31, 31, 1] 119 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 486 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478724 none CN(CC1CCN(C(=O)CC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 44, 29, 29, 29, 29, 18, 5, 18, 1, 1, 1, 1, 1, 29, 63, 80, 80, 90, 90, 119, 119, 119, 119, 119, 63, 63, 63, 44, 44, 29, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 29, 29, 90, 90, 119] 119 rigid atoms, others: [43, 37, 38, 39, 40, 9, 10, 11, 12, 13, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 388 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478724 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478724 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478724/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478724 Building REAL300025478725 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478725' /scratch/stefan/7787258/working/building/REAL300025478725 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478725 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478725/0 /scratch/stefan/7787258/working/building/REAL300025478725 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/617 `/scratch/stefan/7787258/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478725 none CN(CC1CCN(C(=O)C2=CC=CC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 1, 14, 30, 30, 59, 84, 142, 142, 142, 142, 142, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 59, 59, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 393 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478725 none CN(CC1CCN(C(=O)C2=CC=CC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 71, 82, 123, 142, 142, 142, 142, 161, 161, 201, 201, 201, 201, 201, 201, 142, 38, 71, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 123, 123, 142, 142, 142, 142, 142, 201, 201, 201, 201, 142, 142, 38, 38, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 727 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478725 none CN(CC1CCN(C(=O)C2=CC=CC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 43, 71, 71, 114, 143, 201, 201, 201, 201, 201, 43, 43, 43, 27, 27, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 114, 114, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 630 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478725 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478725 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478725/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478725 Building REAL300025478726 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478726' /scratch/stefan/7787258/working/building/REAL300025478726 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478726 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478726/0 /scratch/stefan/7787258/working/building/REAL300025478726 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/618 `/scratch/stefan/7787258/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2C(C)(C)C2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478726 none CN(CC1CCN(C(=O)C2C(C)(C)C2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 12, 29, 29, 54, 73, 117, 117, 117, 117, 117, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 54, 54, 117] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 339 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478726 none CN(CC1CCN(C(=O)C2C(C)(C)C2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 58, 75, 100, 117, 117, 117, 117, 124, 124, 201, 201, 201, 201, 201, 201, 117, 32, 58, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 100, 100, 117, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 32, 32, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 810 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478726 none CN(CC1CCN(C(=O)C2C(C)(C)C2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 15, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 32, 60, 60, 105, 137, 201, 201, 201, 201, 201, 32, 32, 32, 15, 15, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 105, 105, 201] 201 rigid atoms, others: [37, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 619 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478726 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478726 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478726/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478726 Building REAL300025478727 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478727' /scratch/stefan/7787258/working/building/REAL300025478727 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478727 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478727/0 /scratch/stefan/7787258/working/building/REAL300025478727 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/619 `/scratch/stefan/7787258/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1) `REAL300025478727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478727 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 25, 36, 36, 56, 56, 83, 127, 201, 201, 201, 201, 201, 10, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 25, 25, 36, 36, 36, 83, 83, 201, 10, 10, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 561 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: REAL300025478727 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 112, 137, 112, 112, 112, 104, 71, 49, 71, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 201, 112, 112, 112, 112, 112, 104, 104, 71, 71, 71, 25, 25, 1, 112, 112, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 657 number of broken/clashed sets: 39 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478727 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 23, 23, 39, 62, 112, 112, 112, 112, 112, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 39, 39, 112, 1, 1, 10] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 297 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478727 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478727 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478727/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478727 Building REAL300025478728 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478728' /scratch/stefan/7787258/working/building/REAL300025478728 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478728 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478728/0 /scratch/stefan/7787258/working/building/REAL300025478728 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/620 `/scratch/stefan/7787258/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478728 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 44, 76, 163, 163, 163, 163, 163, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 44, 44, 163, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 42, 43, 21, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 395 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478728 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 4, 4, 7, 7, 7, 7, 20, 31, 31, 46, 46, 79, 122, 201, 201, 201, 201, 201, 7, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 7, 7, 20, 20, 31, 31, 31, 79, 79, 201, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 44, 45, 46, 47, 48, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 556 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478728 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 163, 174, 163, 163, 163, 143, 87, 56, 87, 25, 55, 12, 1, 1, 1, 1, 1, 1, 1, 163, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163, 163, 143, 143, 87, 87, 87, 25, 25, 1, 163, 163, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 821 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478728 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478728 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478728/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478728 Building REAL300025478729 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478729' /scratch/stefan/7787258/working/building/REAL300025478729 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478729 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478729/0 /scratch/stefan/7787258/working/building/REAL300025478729 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/621 `/scratch/stefan/7787258/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2C3CCCC32)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478729 none CN(CC1CCN(C(=O)C2C3CCCC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 9, 22, 22, 44, 60, 119, 119, 119, 119, 119, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 44, 44, 119] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 327 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478729 none CN(CC1CCN(C(=O)C2C3CCCC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 66, 72, 108, 119, 119, 119, 119, 122, 122, 201, 201, 201, 201, 201, 119, 36, 66, 13, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 108, 108, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 36, 36, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 812 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478729 none CN(CC1CCN(C(=O)C2C3CCCC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 28, 59, 59, 97, 126, 201, 201, 201, 201, 201, 28, 28, 28, 20, 20, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 97, 97, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 593 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478729 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478729 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478729/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478729 Building REAL300025478730 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478730' /scratch/stefan/7787258/working/building/REAL300025478730 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478730 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478730/0 /scratch/stefan/7787258/working/building/REAL300025478730 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/622 `/scratch/stefan/7787258/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(C#N)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478730 none CN(CC1CCN(C(=O)C2=CC(C#N)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 1, 14, 25, 25, 51, 71, 138, 138, 138, 138, 138, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 1, 1, 51, 51, 138] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 356 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478730 none CN(CC1CCN(C(=O)C2=CC(C#N)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 87, 92, 123, 138, 138, 138, 138, 152, 152, 201, 201, 201, 201, 201, 201, 138, 39, 87, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 123, 123, 138, 138, 138, 138, 138, 201, 201, 201, 138, 138, 39, 39, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 682 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478730 none CN(CC1CCN(C(=O)C2=CC(C#N)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 30, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 14, 47, 66, 66, 108, 138, 201, 201, 201, 201, 201, 47, 47, 47, 30, 30, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 108, 108, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 598 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478730 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478730 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478730/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478730 Building REAL300025478731 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478731' /scratch/stefan/7787258/working/building/REAL300025478731 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478731 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478731/0 /scratch/stefan/7787258/working/building/REAL300025478731 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/623 `/scratch/stefan/7787258/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478731 none CC1=CSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 27, 40, 40, 56, 56, 81, 120, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 27, 27, 40, 40, 40, 81, 81, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 567 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478731 none CC1=CSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 153, 118, 153, 118, 118, 118, 99, 70, 54, 70, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 99, 99, 70, 70, 70, 28, 28, 1, 118, 118] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 686 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478731 none CC1=CSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 34, 53, 118, 118, 118, 118, 118, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 34, 34, 118, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 277 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478731 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478731 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478731/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478731 Building REAL300025478732 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478732' /scratch/stefan/7787258/working/building/REAL300025478732 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478732 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478732/0 /scratch/stefan/7787258/working/building/REAL300025478732 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/624 `/scratch/stefan/7787258/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478732 none CN(CC1CCN(C(=O)CCC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 25, 50, 50, 50, 1, 8, 12, 12, 17, 17, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 29, 29, 50, 50, 50, 50, 50, 50, 50, 1, 1, 17, 17, 43] 177 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 307 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478732 none CN(CC1CCN(C(=O)CCC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 35, 37, 39, 43, 43, 43, 43, 55, 55, 113, 119, 177, 177, 177, 43, 30, 35, 13, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 39, 39, 43, 43, 43, 43, 43, 113, 113, 128, 128, 177, 177, 177, 177, 177, 177, 177, 43, 43, 30, 30, 1] 177 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 773 number of broken/clashed sets: 108 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478732 none CN(CC1CCN(C(=O)CCC2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [99, 72, 50, 50, 50, 50, 33, 12, 33, 6, 1, 1, 1, 1, 1, 50, 99, 122, 122, 136, 136, 177, 177, 177, 177, 177, 99, 99, 99, 72, 72, 50, 50, 50, 50, 50, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 50, 50, 136, 136, 177] 177 rigid atoms, others: [45, 43, 40, 41, 10, 11, 12, 13, 14, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47, 48, 49, 50, 51]) total number of confs: 600 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478732 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478732 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478732/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478732 Building REAL300025478733 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478733' /scratch/stefan/7787258/working/building/REAL300025478733 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478733 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478733/0 /scratch/stefan/7787258/working/building/REAL300025478733 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/625 `/scratch/stefan/7787258/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478733 none CC1=CC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 26, 34, 34, 53, 53, 82, 124, 201, 201, 201, 201, 201, 11, 1, 2, 2, 2, 1, 2, 2, 2, 11, 11, 11, 11, 11, 26, 26, 34, 34, 34, 82, 82, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 574 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: REAL300025478733 none CC1=CC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 146, 119, 146, 119, 119, 119, 105, 72, 50, 72, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 105, 105, 72, 72, 72, 25, 25, 1, 119, 119] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 662 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: REAL300025478733 none CC1=CC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 39, 60, 119, 119, 119, 119, 119, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 39, 39, 119, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 310 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478733 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478733 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478733/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478733 Building REAL300025478734 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478734' /scratch/stefan/7787258/working/building/REAL300025478734 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478734 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478734/0 /scratch/stefan/7787258/working/building/REAL300025478734 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/626 `/scratch/stefan/7787258/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 10, 11, 11, 11, 11, 1, 5, 6, 6, 6, 6, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 10, 10, 11, 11, 1, 1, 6, 6, 10] 16 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 65 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: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 10, 10, 10, 10, 11, 11, 15, 16, 16, 16, 16, 16, 10, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 15, 15, 16, 16, 16, 16, 10, 10, 9, 9, 1] 16 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 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: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 11, 11, 11, 10, 5, 10, 4, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 11, 11, 14, 14, 16] 16 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478734 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478734/1 /scratch/stefan/7787258/working/building/REAL300025478734 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/627 `/scratch/stefan/7787258/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=NNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478734.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 2, 2, 13, 15, 43, 43, 43, 43, 1, 7, 9, 9, 10, 10, 32, 32, 32, 32, 32, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 13, 13, 15, 15, 43, 43, 1, 1, 10, 10, 32] 120 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 27, 32, 32, 32, 32, 39, 39, 74, 76, 120, 120, 120, 120, 32, 24, 26, 13, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 27, 27, 32, 32, 32, 32, 32, 74, 74, 76, 76, 120, 120, 32, 32, 24, 24, 1] 120 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 386 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478734 none CN(CC1CCN(C(=O)CCC2=NNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [81, 63, 42, 42, 42, 42, 31, 15, 31, 8, 1, 1, 1, 1, 1, 1, 42, 81, 94, 94, 97, 97, 120, 120, 120, 120, 120, 81, 81, 81, 63, 63, 42, 42, 42, 43, 42, 15, 15, 8, 8, 1, 1, 42, 42, 97, 97, 120] 120 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 429 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478734 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478734 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478734/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478734/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478734 Building REAL300025478735 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478735' /scratch/stefan/7787258/working/building/REAL300025478735 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478735 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478735/0 /scratch/stefan/7787258/working/building/REAL300025478735 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/628 `/scratch/stefan/7787258/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478735 none CC1=CC=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 24, 35, 35, 48, 48, 78, 114, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 35, 35, 35, 78, 78, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 549 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478735 none CC1=CC=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 162, 137, 162, 137, 137, 137, 115, 82, 52, 82, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 115, 115, 82, 82, 82, 26, 26, 1, 137, 137] 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, 46, 47]) total number of confs: 688 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478735 none CC1=CC=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 19, 19, 41, 64, 137, 137, 137, 137, 137, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 41, 41, 137, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 346 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478735 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478735 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478735/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478735 Building REAL300025478736 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478736' /scratch/stefan/7787258/working/building/REAL300025478736 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478736 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478736/0 /scratch/stefan/7787258/working/building/REAL300025478736 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/629 `/scratch/stefan/7787258/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1) `REAL300025478736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478736 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 26, 37, 37, 51, 51, 78, 122, 201, 201, 201, 201, 201, 10, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 26, 26, 37, 37, 37, 78, 78, 201, 10, 10, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 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: REAL300025478736 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 132, 159, 132, 132, 132, 110, 81, 59, 81, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 110, 110, 81, 81, 81, 30, 30, 1, 132, 132, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 686 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: REAL300025478736 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 40, 65, 132, 132, 132, 132, 132, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 40, 40, 132, 1, 1, 10, 10, 10] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 328 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478736 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478736 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478736/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478736 Building REAL300025478737 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478737' /scratch/stefan/7787258/working/building/REAL300025478737 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478737 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478737/0 /scratch/stefan/7787258/working/building/REAL300025478737 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/630 `/scratch/stefan/7787258/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478737 none CC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 17, 17, 39, 61, 140, 140, 140, 140, 140, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 39, 39, 140, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 342 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478737 none CC=C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 150, 201, 140, 150, 140, 140, 140, 124, 89, 62, 89, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 124, 124, 89, 89, 89, 28, 28, 1, 140, 140] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 772 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478737 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478737 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478737/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478737 Building REAL300025478738 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478738' /scratch/stefan/7787258/working/building/REAL300025478738 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478738 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478738/0 /scratch/stefan/7787258/working/building/REAL300025478738 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/631 `/scratch/stefan/7787258/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478738 none CN(CC1CCN(C(=O)CCC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 20, 35, 35, 35, 35, 1, 8, 12, 12, 15, 16, 38, 38, 38, 38, 38, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 22, 22, 35, 35, 35, 35, 35, 35, 35, 1, 1, 15, 15, 38] 126 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478738 none CN(CC1CCN(C(=O)CCC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [32, 31, 32, 35, 38, 38, 38, 38, 42, 42, 93, 101, 126, 126, 126, 126, 38, 27, 31, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 35, 35, 38, 38, 38, 38, 38, 93, 93, 108, 108, 126, 126, 126, 126, 126, 126, 126, 38, 38, 27, 27, 1] 126 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 555 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478738 none CN(CC1CCN(C(=O)CCC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [72, 54, 35, 35, 35, 35, 22, 8, 22, 4, 1, 1, 1, 1, 1, 1, 35, 72, 89, 89, 98, 98, 126, 126, 126, 126, 126, 72, 72, 72, 54, 54, 35, 35, 35, 35, 35, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 98, 98, 126] 126 rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52]) total number of confs: 428 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478738 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478738 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478738/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478738 Building REAL300025478739 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478739' /scratch/stefan/7787258/working/building/REAL300025478739 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478739 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478739/0 /scratch/stefan/7787258/working/building/REAL300025478739 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/632 `/scratch/stefan/7787258/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478739 none CN(CC1CCN(C(=O)CCC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 24, 48, 48, 48, 48, 1, 9, 13, 13, 19, 20, 40, 40, 40, 40, 40, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 24, 24, 48, 48, 48, 1, 1, 19, 19, 40] 183 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 243 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478739 none CN(CC1CCN(C(=O)CCC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 34, 37, 40, 40, 40, 40, 53, 53, 105, 108, 183, 183, 183, 183, 40, 26, 32, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 37, 37, 40, 40, 40, 40, 40, 105, 105, 108, 108, 183, 183, 183, 40, 40, 26, 26, 1] 183 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 578 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478739 none CN(CC1CCN(C(=O)CCC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [97, 73, 47, 47, 47, 47, 25, 8, 25, 4, 1, 1, 1, 1, 1, 1, 47, 97, 117, 117, 137, 137, 183, 183, 183, 183, 183, 97, 97, 97, 73, 73, 47, 47, 47, 48, 47, 8, 8, 4, 4, 1, 1, 1, 47, 47, 137, 137, 183] 183 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 590 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478739 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478739 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478739/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478739 Building REAL300025478740 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478740' /scratch/stefan/7787258/working/building/REAL300025478740 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478740 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478740/0 /scratch/stefan/7787258/working/building/REAL300025478740 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/633 `/scratch/stefan/7787258/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC(F)(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478740 none CN(CC1CCN(C(=O)C2CC(F)(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 1, 13, 29, 29, 49, 64, 111, 111, 111, 111, 111, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 49, 49, 111] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 317 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478740 none CN(CC1CCN(C(=O)C2CC(F)(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 65, 71, 103, 111, 111, 111, 111, 117, 117, 201, 201, 201, 201, 201, 111, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 103, 103, 111, 111, 111, 111, 111, 201, 201, 201, 201, 201, 111, 111, 37, 37, 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: 787 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478740 none CN(CC1CCN(C(=O)C2CC(F)(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 45, 74, 74, 112, 140, 201, 201, 201, 201, 201, 45, 45, 45, 24, 24, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 112, 112, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 603 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478740 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478740 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478740/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478740 Building REAL300025478741 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478741' /scratch/stefan/7787258/working/building/REAL300025478741 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478741 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478741/0 /scratch/stefan/7787258/working/building/REAL300025478741 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/634 `/scratch/stefan/7787258/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478741 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 27, 36, 36, 45, 45, 72, 113, 201, 201, 201, 201, 201, 10, 1, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 36, 36, 36, 72, 72, 201, 10, 10, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 48, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478741 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 110, 116, 110, 110, 110, 103, 72, 52, 72, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 103, 103, 72, 72, 72, 29, 29, 1, 110, 110, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 774 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478741 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 28, 46, 110, 110, 110, 110, 110, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 110, 1, 1, 10, 10] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 269 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478741 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478741 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478741/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478741 Building REAL300025478742 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478742' /scratch/stefan/7787258/working/building/REAL300025478742 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478742 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478742/0 /scratch/stefan/7787258/working/building/REAL300025478742 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/635 `/scratch/stefan/7787258/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1) `REAL300025478742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478742 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 23, 23, 40, 62, 122, 122, 122, 122, 122, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 40, 40, 122, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 44, 34, 21, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 311 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: REAL300025478742 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 6, 6, 6, 6, 19, 31, 31, 54, 54, 81, 119, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 19, 19, 31, 31, 31, 81, 81, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 45, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 543 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: REAL300025478742 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 122, 131, 122, 122, 122, 101, 78, 57, 78, 27, 57, 12, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 101, 101, 78, 78, 78, 27, 27, 1, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 765 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478742 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478742 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478742/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478742 Building REAL300025478743 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478743' /scratch/stefan/7787258/working/building/REAL300025478743 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478743 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478743/0 /scratch/stefan/7787258/working/building/REAL300025478743 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/636 `/scratch/stefan/7787258/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478743 none CN(CC1CCN(C(=O)CC2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 40, 40, 40, 40, 40, 1, 9, 13, 13, 19, 19, 49, 49, 49, 49, 49, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 19, 19, 49] 158 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 244 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478743 none CN(CC1CCN(C(=O)CC2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 41, 44, 49, 49, 49, 49, 72, 72, 143, 158, 158, 158, 158, 158, 49, 33, 39, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 44, 44, 49, 49, 49, 49, 49, 143, 143, 158, 158, 158, 158, 158, 158, 158, 158, 158, 49, 49, 33, 33, 1] 158 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 653 number of broken/clashed sets: 94 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478743 none CN(CC1CCN(C(=O)CC2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [84, 62, 40, 40, 40, 40, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 40, 84, 107, 107, 119, 119, 158, 158, 158, 158, 158, 84, 84, 84, 62, 62, 40, 40, 40, 40, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 119, 119, 158] 158 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 497 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478743 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478743 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478743/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478743 Building REAL300025478744 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478744' /scratch/stefan/7787258/working/building/REAL300025478744 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478744 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478744/0 /scratch/stefan/7787258/working/building/REAL300025478744 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/637 `/scratch/stefan/7787258/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478744 none CC1=NNC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 9, 9, 15, 15, 15, 15, 35, 46, 46, 47, 47, 79, 106, 201, 201, 201, 201, 201, 15, 1, 2, 2, 2, 1, 4, 4, 15, 15, 15, 15, 15, 35, 35, 46, 46, 46, 79, 79, 201, 15, 15, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 568 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: REAL300025478744 none CC1=NNC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 102, 111, 102, 102, 102, 88, 60, 40, 60, 25, 40, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 102, 88, 88, 60, 60, 60, 25, 25, 1, 102, 102, 201] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 856 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: REAL300025478744 none CC1=NNC(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 19, 30, 102, 102, 102, 102, 102, 1, 15, 15, 15, 15, 15, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 19, 19, 102, 1, 1, 15] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 241 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478744 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478744 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478744/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478744 Building REAL300025478745 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478745' /scratch/stefan/7787258/working/building/REAL300025478745 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478745 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478745/0 /scratch/stefan/7787258/working/building/REAL300025478745 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/638 `/scratch/stefan/7787258/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C=C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478745 none CN(CC1CCN(C(=O)C=C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 1, 13, 28, 28, 54, 78, 160, 160, 160, 160, 160, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 54, 54, 160] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478745 none CN(CC1CCN(C(=O)C=C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 78, 90, 142, 160, 160, 160, 160, 168, 168, 201, 201, 201, 201, 160, 36, 78, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 142, 142, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 160, 160, 36, 36, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 799 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478745 none CN(CC1CCN(C(=O)C=C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 26, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 13, 36, 63, 63, 101, 133, 201, 201, 201, 201, 201, 36, 36, 36, 26, 26, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 101, 101, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478745 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478745 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478745/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478745 Building REAL300025478746 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478746' /scratch/stefan/7787258/working/building/REAL300025478746 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478746 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478746/0 /scratch/stefan/7787258/working/building/REAL300025478746 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/639 `/scratch/stefan/7787258/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478746 none CN(CC1CCN(C(=O)C2=CN=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 1, 14, 32, 32, 56, 72, 122, 122, 122, 122, 122, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 56, 56, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 344 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478746 none CN(CC1CCN(C(=O)C2=CN=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 61, 70, 108, 122, 122, 122, 122, 135, 135, 201, 201, 201, 201, 201, 201, 122, 37, 61, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 108, 108, 122, 122, 122, 122, 122, 201, 201, 201, 122, 122, 37, 37, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 679 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478746 none CN(CC1CCN(C(=O)C2=CN=CC(F)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 30, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 52, 83, 83, 122, 149, 201, 201, 201, 201, 201, 52, 52, 52, 30, 30, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 122, 122, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 638 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478746 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478746 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478746/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478746 Building REAL300025478747 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478747' /scratch/stefan/7787258/working/building/REAL300025478747 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478747 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478747/0 /scratch/stefan/7787258/working/building/REAL300025478747 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/640 `/scratch/stefan/7787258/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)CC) `REAL300025478747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478747 none CCC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 31, 49, 119, 119, 119, 119, 119, 1, 9, 9, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 31, 31, 119, 1, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 303 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478747 none CCC(=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 195, 128, 119, 128, 119, 119, 119, 108, 76, 50, 76, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 119, 195, 195, 201, 201, 201, 201, 201, 195, 119, 119, 119, 119, 119, 108, 108, 76, 76, 76, 27, 27, 1, 119, 119, 195, 195, 195, 195, 195] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 751 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478747 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478747 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478747/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478747 Building REAL300025478748 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478748' /scratch/stefan/7787258/working/building/REAL300025478748 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478748 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478748/0 /scratch/stefan/7787258/working/building/REAL300025478748 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/641 `/scratch/stefan/7787258/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(=O)NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478748 none CN(CC1CCN(C(=O)C2=CC(=O)NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 1, 15, 32, 32, 61, 89, 159, 159, 159, 159, 159, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 61, 61, 159] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 414 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478748 none CN(CC1CCN(C(=O)C2=CC(=O)NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 89, 104, 150, 159, 159, 159, 159, 167, 167, 201, 201, 201, 201, 201, 201, 159, 37, 89, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 150, 150, 159, 159, 159, 159, 159, 201, 201, 201, 201, 159, 159, 37, 37, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 718 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478748 none CN(CC1CCN(C(=O)C2=CC(=O)NC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 40, 68, 68, 106, 138, 201, 201, 201, 201, 201, 40, 40, 40, 24, 24, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 106, 106, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 595 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478748 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478748 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478748/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478748 Building REAL300025478749 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478749' /scratch/stefan/7787258/working/building/REAL300025478749 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478749 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478749/0 /scratch/stefan/7787258/working/building/REAL300025478749 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/642 `/scratch/stefan/7787258/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478749 none CC(C)=C(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 2, 9, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 38, 62, 122, 122, 122, 122, 122, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 38, 38, 122, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 315 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478749 none CC(C)=C(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 140, 201, 122, 140, 122, 122, 122, 107, 75, 54, 75, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 107, 107, 75, 75, 75, 27, 27, 1, 122, 122] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 789 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478749 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478749 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478749/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478749 Building REAL300025478750 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478750' /scratch/stefan/7787258/working/building/REAL300025478750 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478750 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478750/0 /scratch/stefan/7787258/working/building/REAL300025478750 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/643 `/scratch/stefan/7787258/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478750 none CN(CC1CCN(C(=O)C2CCNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 13, 34, 34, 63, 93, 155, 155, 155, 155, 155, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 63, 63, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 416 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: REAL300025478750 none CN(CC1CCN(C(=O)C2CCNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 81, 97, 133, 155, 155, 155, 155, 164, 164, 201, 201, 201, 201, 201, 201, 155, 37, 81, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 133, 133, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 37, 37, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 780 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: REAL300025478750 none CN(CC1CCN(C(=O)C2CCNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 33, 62, 62, 103, 141, 201, 201, 201, 201, 201, 33, 33, 33, 18, 18, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 103, 103, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 581 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478750 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478750 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478750/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478750 Building REAL300025478751 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478751' /scratch/stefan/7787258/working/building/REAL300025478751 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478751 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478751/0 /scratch/stefan/7787258/working/building/REAL300025478751 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/644 `/scratch/stefan/7787258/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478751 none CN(CC1CCN(C(=O)C2=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 1, 14, 32, 32, 63, 94, 182, 182, 182, 182, 182, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 63, 63, 182] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478751 none CN(CC1CCN(C(=O)C2=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 79, 95, 153, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 182, 39, 79, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 153, 153, 182, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 182, 182, 39, 39, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 813 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478751 none CN(CC1CCN(C(=O)C2=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 17, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 28, 54, 54, 91, 126, 201, 201, 201, 201, 201, 28, 28, 28, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 91, 91, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 549 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478751 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478751 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478751/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478751 Building REAL300025478752 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478752' /scratch/stefan/7787258/working/building/REAL300025478752 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478752 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478752/0 /scratch/stefan/7787258/working/building/REAL300025478752 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/645 `/scratch/stefan/7787258/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(F)=C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478752 none CN(CC1CCN(C(=O)C(F)=C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 12, 1, 12, 27, 27, 45, 61, 120, 120, 120, 120, 120, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 12, 12, 12, 12, 1, 1, 45, 45, 120] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 325 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478752 none CN(CC1CCN(C(=O)C(F)=C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 62, 70, 111, 120, 120, 120, 120, 149, 149, 201, 201, 201, 201, 201, 201, 120, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 111, 111, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 31, 31, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 812 number of broken/clashed sets: 42 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478752 none CN(CC1CCN(C(=O)C(F)=C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 30, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 46, 80, 80, 117, 146, 201, 201, 201, 201, 201, 46, 46, 46, 30, 30, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 117, 117, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 624 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478752 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478752 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478752/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478752 Building REAL300025478753 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478753' /scratch/stefan/7787258/working/building/REAL300025478753 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478753 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478753/0 /scratch/stefan/7787258/working/building/REAL300025478753 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/646 `/scratch/stefan/7787258/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478753 none CN(CC1CCN(C(=O)C2=CN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 9, 22, 22, 45, 67, 131, 131, 131, 131, 131, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 45, 45, 131] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 336 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478753 none CN(CC1CCN(C(=O)C2=CN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 70, 79, 120, 131, 131, 131, 131, 139, 139, 201, 201, 201, 201, 201, 131, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 120, 120, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 131, 131, 37, 37, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 677 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478753 none CN(CC1CCN(C(=O)C2=CN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 23, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 35, 59, 59, 102, 136, 201, 201, 201, 201, 201, 35, 35, 35, 23, 23, 10, 10, 10, 10, 10, 1, 2, 2, 2, 1, 1, 10, 10, 102, 102, 201] 201 rigid atoms, others: [36, 7, 40, 9, 10, 11, 12, 13, 14, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 618 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478753 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478753 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478753/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478753 Building REAL300025478754 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478754' /scratch/stefan/7787258/working/building/REAL300025478754 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478754 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478754/0 /scratch/stefan/7787258/working/building/REAL300025478754 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/647 `/scratch/stefan/7787258/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478754 none CN(CC1CCN(C(=O)C2=CN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 6, 6, 1, 11, 29, 29, 48, 74, 155, 155, 155, 155, 155, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1, 1, 48, 48, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 370 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: REAL300025478754 none CN(CC1CCN(C(=O)C2=CN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 75, 88, 138, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 155, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 138, 138, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 155, 155, 38, 38, 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: 805 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: REAL300025478754 none CN(CC1CCN(C(=O)C2=CN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 5, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 28, 60, 60, 92, 127, 201, 201, 201, 201, 201, 28, 28, 28, 18, 18, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 5, 5, 92, 92, 201] 201 rigid atoms, others: [36, 7, 40, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 555 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478754 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478754 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478754/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478754 Building REAL300025478755 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478755' /scratch/stefan/7787258/working/building/REAL300025478755 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478755 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478755/0 /scratch/stefan/7787258/working/building/REAL300025478755 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/648 `/scratch/stefan/7787258/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2COC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478755 none CN(CC1CCN(C(=O)CC2COC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 17, 30, 30, 30, 30, 30, 1, 9, 13, 13, 19, 20, 39, 39, 39, 39, 39, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 17, 17, 30, 30, 30, 30, 30, 1, 1, 19, 19, 39] 91 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478755 none CN(CC1CCN(C(=O)CC2COC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [31, 29, 31, 34, 39, 39, 39, 39, 46, 46, 76, 91, 91, 91, 91, 91, 39, 24, 29, 12, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 34, 34, 39, 39, 39, 39, 39, 76, 76, 91, 91, 91, 91, 91, 39, 39, 24, 24, 1] 91 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 358 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478755 none CN(CC1CCN(C(=O)CC2COC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [55, 42, 30, 30, 30, 30, 18, 6, 18, 1, 1, 1, 1, 1, 1, 1, 30, 55, 63, 63, 73, 73, 91, 91, 91, 91, 91, 55, 55, 55, 42, 42, 30, 30, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 30, 30, 73, 73, 91] 91 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48]) total number of confs: 307 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478755 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478755 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478755/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478755 Building REAL300025478756 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478756' /scratch/stefan/7787258/working/building/REAL300025478756 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478756 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478756/0 /scratch/stefan/7787258/working/building/REAL300025478756 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/649 `/scratch/stefan/7787258/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478756 none CC1=C(C)OC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 21, 35, 35, 50, 50, 75, 117, 201, 201, 201, 201, 201, 8, 1, 2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 35, 35, 35, 75, 75, 201, 8, 8, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 530 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: REAL300025478756 none CC1=C(C)OC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 194, 168, 194, 168, 168, 168, 150, 101, 62, 101, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 150, 150, 101, 101, 101, 29, 29, 1, 168, 168, 201] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 731 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: REAL300025478756 none CC1=C(C)OC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 5, 14, 14, 30, 30, 53, 84, 168, 168, 168, 168, 168, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 53, 53, 168, 1, 1, 8] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 407 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478756 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478756 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478756/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478756 Building REAL300025478757 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478757' /scratch/stefan/7787258/working/building/REAL300025478757 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478757 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478757/0 /scratch/stefan/7787258/working/building/REAL300025478757 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/650 `/scratch/stefan/7787258/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478757 none CN(CC1CCN(C(=O)CC2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 19, 44, 44, 44, 44, 44, 1, 8, 11, 11, 17, 17, 41, 41, 41, 41, 41, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 20, 20, 45, 45, 44, 45, 1, 1, 17, 17, 41] 154 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478757 none CN(CC1CCN(C(=O)CC2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 37, 41, 41, 41, 41, 46, 46, 111, 154, 154, 154, 154, 154, 41, 28, 35, 13, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 37, 37, 41, 41, 41, 41, 41, 111, 111, 154, 154, 154, 154, 41, 41, 28, 28, 1] 154 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 510 number of broken/clashed sets: 103 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478757 none CN(CC1CCN(C(=O)CC2=CC=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [87, 70, 44, 44, 44, 44, 25, 8, 25, 1, 1, 1, 1, 1, 1, 1, 44, 87, 101, 101, 119, 119, 154, 154, 154, 154, 154, 87, 87, 87, 70, 70, 44, 44, 44, 45, 45, 8, 8, 1, 1, 1, 1, 45, 44, 119, 119, 154] 154 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 544 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478757 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478757 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478757/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478757 Building REAL300025478758 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478758' /scratch/stefan/7787258/working/building/REAL300025478758 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478758 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478758/0 /scratch/stefan/7787258/working/building/REAL300025478758 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/651 `/scratch/stefan/7787258/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478758 none CN(CC1CCN(C(=O)C2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 1, 15, 34, 34, 73, 104, 175, 175, 175, 175, 175, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 73, 73, 175] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 473 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478758 none CN(CC1CCN(C(=O)C2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 80, 102, 157, 175, 175, 175, 175, 196, 196, 201, 201, 201, 201, 201, 175, 35, 80, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 157, 157, 175, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 35, 35, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 804 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478758 none CN(CC1CCN(C(=O)C2CCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 30, 59, 59, 107, 141, 201, 201, 201, 201, 201, 30, 30, 30, 18, 18, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 107, 107, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 604 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478758 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478758 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478758/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478758 Building REAL300025478759 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478759' /scratch/stefan/7787258/working/building/REAL300025478759 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478759 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478759/0 /scratch/stefan/7787258/working/building/REAL300025478759 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/652 `/scratch/stefan/7787258/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O) `REAL300025478759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478759 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 23, 35, 35, 52, 52, 85, 127, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 35, 35, 35, 85, 85, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 570 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478759 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 162, 151, 162, 151, 151, 151, 139, 94, 62, 94, 28, 61, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151, 151, 139, 139, 94, 94, 94, 28, 28, 1, 151, 151] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 780 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478759 none CC1=NNC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 44, 69, 151, 151, 151, 151, 151, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 44, 44, 151, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478759 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478759 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478759/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478759 Building REAL300025478760 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478760' /scratch/stefan/7787258/working/building/REAL300025478760 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478760 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478760/0 /scratch/stefan/7787258/working/building/REAL300025478760 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/653 `/scratch/stefan/7787258/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(SC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478760 none CCC(SC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 2, 4, 12, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 34, 57, 152, 152, 152, 152, 152, 1, 7, 7, 7, 7, 7, 4, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 34, 34, 152, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 357 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478760 none CCC(SC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 187, 192, 201, 152, 187, 152, 152, 152, 137, 93, 65, 93, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 152, 192, 192, 192, 192, 192, 192, 201, 201, 201, 152, 152, 152, 152, 152, 137, 137, 93, 93, 93, 29, 29, 1, 152, 152] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 764 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478760 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478760 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478760/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478760 Building REAL300025478761 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478761' /scratch/stefan/7787258/working/building/REAL300025478761 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478761 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478761/0 /scratch/stefan/7787258/working/building/REAL300025478761 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/654 `/scratch/stefan/7787258/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=C1) `REAL300025478761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478761 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 47, 76, 164, 164, 164, 164, 164, 1, 5, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 47, 47, 164, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 404 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478761 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 7, 8, 8, 8, 8, 16, 25, 25, 34, 34, 66, 108, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 8, 8, 16, 16, 25, 25, 25, 66, 66, 201, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478761 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 164, 174, 164, 164, 164, 142, 96, 57, 96, 26, 57, 13, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 142, 142, 96, 96, 96, 26, 26, 1, 164, 164, 201, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 806 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478761 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478761 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478761/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478761 Building REAL300025478762 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478762' /scratch/stefan/7787258/working/building/REAL300025478762 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478762 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478762/0 /scratch/stefan/7787258/working/building/REAL300025478762 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/655 `/scratch/stefan/7787258/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1) `REAL300025478762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478762 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 22, 30, 30, 53, 53, 86, 126, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 1, 9, 9, 9, 9, 9, 22, 22, 30, 30, 30, 86, 86, 201, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 570 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478762 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 140, 179, 140, 140, 140, 129, 83, 55, 83, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 129, 129, 83, 83, 83, 27, 27, 1, 140, 140, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 718 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478762 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 42, 68, 140, 140, 140, 140, 140, 1, 9, 9, 8, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 42, 42, 140, 1, 1, 9] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 355 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478762 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478762 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478762/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478762 Building REAL300025478763 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478763' /scratch/stefan/7787258/working/building/REAL300025478763 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478763 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478763/0 /scratch/stefan/7787258/working/building/REAL300025478763 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/656 `/scratch/stefan/7787258/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478763 none CN(CC1CCN(C(=O)C2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 1, 14, 30, 30, 72, 97, 172, 172, 172, 172, 172, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 72, 72, 172] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 472 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478763 none CN(CC1CCN(C(=O)C2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 78, 98, 143, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 172, 40, 78, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 143, 143, 172, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 40, 40, 1] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 807 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478763 none CN(CC1CCN(C(=O)C2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 28, 51, 51, 100, 131, 201, 201, 201, 201, 201, 28, 28, 28, 13, 13, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 5, 100, 100, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 594 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478763 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478763 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478763/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478763 Building REAL300025478764 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478764' /scratch/stefan/7787258/working/building/REAL300025478764 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478764 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478764/0 /scratch/stefan/7787258/working/building/REAL300025478764 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/657 `/scratch/stefan/7787258/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(C#N)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478764 none CN(CC1CCN(C(=O)C2=CC=C(C#N)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 1, 13, 25, 25, 51, 68, 119, 119, 119, 119, 119, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 1, 1, 51, 51, 119] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478764 none CN(CC1CCN(C(=O)C2=CC=C(C#N)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 66, 70, 105, 119, 119, 119, 119, 139, 139, 201, 201, 201, 201, 201, 201, 119, 36, 66, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 105, 105, 119, 119, 119, 119, 119, 201, 201, 201, 119, 119, 36, 36, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 679 number of broken/clashed sets: 79 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478764 none CN(CC1CCN(C(=O)C2=CC=C(C#N)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 27, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 43, 70, 70, 114, 141, 201, 201, 201, 201, 201, 43, 43, 43, 27, 27, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 114, 114, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 604 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478764 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478764 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478764/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478764 Building REAL300025478765 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478765' /scratch/stefan/7787258/working/building/REAL300025478765 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478765 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478765/0 /scratch/stefan/7787258/working/building/REAL300025478765 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/658 `/scratch/stefan/7787258/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478765 none CCC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 49, 55, 18, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 24, 34, 72, 72, 72, 72, 72, 1, 59, 59, 59, 59, 59, 55, 55, 55, 55, 18, 18, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 24, 24, 72, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 343 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478765 none CCC(C)OCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 201, 161, 73, 72, 73, 72, 72, 72, 59, 46, 35, 46, 18, 35, 12, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 161, 72, 72, 72, 72, 72, 59, 59, 46, 46, 46, 18, 18, 1, 72, 72] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 732 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478765 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478765 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478765/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478765 Building REAL300025478766 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478766' /scratch/stefan/7787258/working/building/REAL300025478766 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478766 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478766/0 /scratch/stefan/7787258/working/building/REAL300025478766 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/659 `/scratch/stefan/7787258/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478766 none CN(CC1CCN(C(=O)[C@H]2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 1, 14, 30, 30, 72, 97, 172, 172, 172, 172, 172, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 72, 72, 172] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 471 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478766 none CN(CC1CCN(C(=O)[C@H]2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 79, 98, 143, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 172, 40, 79, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 143, 143, 172, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 40, 40, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 807 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478766 none CN(CC1CCN(C(=O)[C@H]2CC2(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 27, 51, 51, 100, 131, 201, 201, 201, 201, 201, 27, 27, 27, 13, 13, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 5, 5, 100, 100, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 595 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478766 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478766 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478766/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478766 Building REAL300025478767 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478767' /scratch/stefan/7787258/working/building/REAL300025478767 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478767 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478767/0 /scratch/stefan/7787258/working/building/REAL300025478767 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/660 `/scratch/stefan/7787258/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478767 none CC1=CC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 9, 9, 13, 13, 13, 13, 32, 43, 43, 48, 48, 73, 114, 201, 201, 201, 201, 201, 13, 1, 2, 2, 2, 1, 1, 7, 7, 13, 13, 13, 13, 13, 32, 32, 43, 43, 43, 73, 73, 201, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 553 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478767 none CC1=CC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 133, 116, 133, 116, 116, 116, 105, 71, 46, 71, 27, 46, 12, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 182, 182, 116, 116, 116, 116, 116, 105, 105, 71, 71, 71, 27, 27, 1, 116, 116] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 833 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478767 none CC1=CC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 33, 48, 116, 116, 116, 116, 116, 1, 13, 13, 13, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 33, 33, 116, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 300 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478767 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478767 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478767/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478767 Building REAL300025478768 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478768' /scratch/stefan/7787258/working/building/REAL300025478768 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478768 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478768/0 /scratch/stefan/7787258/working/building/REAL300025478768 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/661 `/scratch/stefan/7787258/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(C)(O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478768 none CN(CC1CCN(C(=O)CC(C)(O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 12, 12, 12, 12, 12, 1, 8, 10, 10, 13, 13, 24, 24, 24, 24, 24, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 10, 10, 12, 12, 12, 36, 12, 12, 12, 12, 12, 1, 1, 13, 13, 24] 105 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 145 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: REAL300025478768 none CN(CC1CCN(C(=O)CC(C)(O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 22, 24, 24, 24, 24, 24, 24, 33, 35, 35, 35, 35, 35, 24, 20, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 22, 22, 24, 24, 24, 24, 24, 33, 33, 35, 35, 35, 105, 35, 35, 35, 35, 35, 24, 24, 20, 20, 1] 105 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 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: REAL300025478768 none CN(CC1CCN(C(=O)CC(C)(O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 12, 12, 12, 12, 9, 5, 9, 2, 1, 2, 2, 1, 1, 1, 12, 20, 22, 22, 25, 25, 35, 35, 35, 35, 35, 20, 20, 20, 18, 18, 12, 12, 12, 12, 12, 5, 5, 2, 2, 2, 6, 1, 1, 1, 1, 1, 12, 12, 25, 25, 35] 105 rigid atoms, others: [45, 10, 43, 44, 13, 14, 15, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478768 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478768 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478768/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478768 Building REAL300025478769 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478769' /scratch/stefan/7787258/working/building/REAL300025478769 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478769 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478769/0 /scratch/stefan/7787258/working/building/REAL300025478769 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/662 `/scratch/stefan/7787258/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCO1) `REAL300025478769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478769 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 17, 29, 29, 58, 58, 84, 125, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 17, 17, 29, 29, 29, 84, 84, 201, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 558 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478769 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 137, 151, 137, 137, 137, 116, 82, 57, 82, 26, 57, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 116, 116, 82, 82, 82, 26, 26, 1, 137, 137, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 677 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478769 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 27, 27, 46, 71, 137, 137, 137, 137, 137, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 46, 46, 137, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 347 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478769 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478769 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478769/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478769 Building REAL300025478770 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478770' /scratch/stefan/7787258/working/building/REAL300025478770 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478770 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478770/0 /scratch/stefan/7787258/working/building/REAL300025478770 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/663 `/scratch/stefan/7787258/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478770 none CSC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 8, 10, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 23, 36, 98, 98, 98, 98, 98, 1, 21, 21, 21, 10, 10, 10, 10, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 98, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 263 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478770 none CSC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 179, 120, 98, 120, 98, 98, 98, 86, 61, 41, 61, 26, 41, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 179, 179, 179, 179, 179, 179, 98, 98, 98, 98, 98, 86, 86, 61, 61, 61, 26, 26, 1, 98, 98] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 803 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478770 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478770 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478770/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478770 Building REAL300025478771 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478771' /scratch/stefan/7787258/working/building/REAL300025478771 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478771 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478771/0 /scratch/stefan/7787258/working/building/REAL300025478771 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/664 `/scratch/stefan/7787258/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478771 none CN(CC1CCN(C(=O)CN2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 25, 25, 25, 25, 1, 9, 13, 13, 16, 16, 36, 36, 36, 36, 36, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 16, 16, 36] 77 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 158 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: REAL300025478771 none CN(CC1CCN(C(=O)CN2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [30, 29, 30, 32, 36, 36, 36, 36, 46, 46, 77, 77, 77, 77, 77, 77, 36, 26, 29, 13, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 32, 32, 36, 36, 36, 36, 36, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 36, 36, 26, 26, 1] 77 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 317 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: REAL300025478771 none CN(CC1CCN(C(=O)CN2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [47, 38, 25, 25, 25, 25, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 25, 47, 56, 56, 59, 59, 77, 77, 77, 77, 77, 47, 47, 47, 38, 38, 25, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 59, 59, 77] 77 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50, 51]) total number of confs: 252 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478771 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478771 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478771/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478771 Building REAL300025478772 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478772' /scratch/stefan/7787258/working/building/REAL300025478772 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478772 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478772/0 /scratch/stefan/7787258/working/building/REAL300025478772 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/665 `/scratch/stefan/7787258/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478772 none CN(CC1CCN(C(=O)[C@@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 14, 32, 32, 60, 88, 146, 146, 146, 146, 146, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 60, 60, 146] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 404 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: REAL300025478772 none CN(CC1CCN(C(=O)[C@@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 69, 85, 132, 146, 146, 146, 146, 173, 173, 201, 201, 201, 201, 201, 146, 32, 69, 13, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 132, 132, 146, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 146, 146, 32, 32, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 811 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: REAL300025478772 none CN(CC1CCN(C(=O)[C@@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 47, 79, 79, 117, 152, 201, 201, 201, 201, 201, 47, 47, 47, 26, 26, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 117, 117, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 613 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478772 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478772 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478772/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478772 Building REAL300025478773 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478773' /scratch/stefan/7787258/working/building/REAL300025478773 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478773 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478773/0 /scratch/stefan/7787258/working/building/REAL300025478773 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/666 `/scratch/stefan/7787258/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1) `REAL300025478773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478773 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 20, 20, 42, 70, 158, 158, 158, 158, 158, 1, 7, 9, 9, 9, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 42, 42, 158, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 379 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478773 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 6, 9, 9, 9, 9, 22, 29, 29, 44, 44, 75, 114, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 9, 9, 9, 22, 22, 29, 29, 29, 75, 75, 201, 9, 9, 1, 1] 201 rigid atoms, others: [1, 46, 47, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 542 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478773 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 158, 179, 158, 158, 158, 142, 93, 56, 93, 27, 56, 13, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 158, 142, 142, 93, 93, 93, 27, 27, 1, 158, 158, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 810 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478773 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478773 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478773/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478773 Building REAL300025478774 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478774' /scratch/stefan/7787258/working/building/REAL300025478774 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478774 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478774/0 /scratch/stefan/7787258/working/building/REAL300025478774 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/667 `/scratch/stefan/7787258/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(NC(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478774 none CN(CC1CCN(C(=O)C2(NC(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 5, 12, 12, 15, 15, 23, 23, 23, 23, 23, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 15, 15, 23] 28 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 83 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: REAL300025478774 none CN(CC1CCN(C(=O)C2(NC(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 22, 23, 23, 23, 23, 24, 24, 28, 28, 28, 28, 28, 28, 23, 18, 20, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 22, 22, 23, 23, 23, 23, 23, 28, 28, 28, 28, 28, 28, 28, 23, 23, 18, 18, 1] 28 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 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: REAL300025478774 none CN(CC1CCN(C(=O)C2(NC(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 3, 3, 3, 1, 1, 6, 11, 18, 18, 20, 20, 28, 28, 28, 28, 28, 11, 11, 11, 8, 8, 6, 6, 6, 6, 6, 3, 3, 3, 1, 1, 1, 1, 6, 6, 20, 20, 28] 28 rigid atoms, others: [7, 40, 9, 10, 43, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478774 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478774 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478774/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478774 Building REAL300025478775 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478775' /scratch/stefan/7787258/working/building/REAL300025478775 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478775 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478775/0 /scratch/stefan/7787258/working/building/REAL300025478775 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/668 `/scratch/stefan/7787258/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2COCCN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478775 none CN(CC1CCN(C(=O)C2COCCN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 1, 16, 36, 36, 83, 114, 175, 175, 175, 175, 175, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 83, 83, 175] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 497 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478775 none CN(CC1CCN(C(=O)C2COCCN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 79, 104, 153, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 175, 36, 79, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 153, 153, 175, 175, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 36, 36, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 804 number of broken/clashed sets: 86 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478775 none CN(CC1CCN(C(=O)C2COCCN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 27, 51, 51, 107, 142, 201, 201, 201, 201, 201, 27, 27, 27, 11, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 107, 107, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 592 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478775 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478775 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478775/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478775 Building REAL300025478776 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478776' /scratch/stefan/7787258/working/building/REAL300025478776 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478776 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478776/0 /scratch/stefan/7787258/working/building/REAL300025478776 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/669 `/scratch/stefan/7787258/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478776 none CC1=NSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 26, 37, 37, 51, 51, 80, 117, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 9, 9, 9, 9, 9, 26, 26, 37, 37, 37, 80, 80, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 562 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: REAL300025478776 none CC1=NSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 146, 117, 146, 117, 117, 117, 105, 71, 52, 71, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 117, 117, 117, 117, 117, 105, 105, 71, 71, 71, 29, 29, 1, 117, 117] 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, 43, 44]) total number of confs: 674 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: REAL300025478776 none CC1=NSC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 37, 54, 117, 117, 117, 117, 117, 1, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 37, 37, 117, 1, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 292 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478776 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478776 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478776/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478776 Building REAL300025478777 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478777' /scratch/stefan/7787258/working/building/REAL300025478777 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478777 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478777/0 /scratch/stefan/7787258/working/building/REAL300025478777 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/670 `/scratch/stefan/7787258/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478777 none C#CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 25, 38, 93, 93, 93, 93, 93, 1, 16, 15, 15, 12, 12, 11, 11, 9, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 93, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478777 none C#CCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 182, 178, 107, 93, 107, 93, 93, 93, 80, 56, 44, 56, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 182, 182, 182, 182, 178, 178, 93, 93, 93, 93, 93, 80, 80, 56, 56, 56, 27, 27, 1, 93, 93] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 876 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478777 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478777 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478777/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478777 Building REAL300025478778 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478778' /scratch/stefan/7787258/working/building/REAL300025478778 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478778 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478778/0 /scratch/stefan/7787258/working/building/REAL300025478778 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/671 `/scratch/stefan/7787258/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)COC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478778 none CN(CC1CCN(C(=O)COC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 16, 17, 17, 17, 1, 9, 12, 12, 16, 16, 37, 37, 37, 37, 37, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 16, 16, 37] 59 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 146 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: REAL300025478778 none CN(CC1CCN(C(=O)COC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 31, 32, 34, 37, 37, 37, 37, 45, 45, 59, 59, 59, 59, 59, 37, 27, 31, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 37, 37, 37, 37, 37, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 37, 37, 27, 27, 1] 59 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478778 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478778 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478778/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478778 Building REAL300025478779 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478779' /scratch/stefan/7787258/working/building/REAL300025478779 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478779 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478779/0 /scratch/stefan/7787258/working/building/REAL300025478779 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/672 `/scratch/stefan/7787258/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNC(C#N)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478779 none CN(CC1CCN(C(=O)C2=CNC(C#N)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 1, 12, 27, 27, 51, 73, 126, 126, 126, 126, 126, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 51, 51, 126] 179 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 338 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478779 none CN(CC1CCN(C(=O)C2=CNC(C#N)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [89, 80, 89, 119, 126, 126, 126, 126, 133, 133, 179, 179, 179, 179, 179, 179, 126, 38, 80, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 119, 119, 126, 126, 126, 126, 126, 179, 179, 179, 126, 126, 38, 38, 1] 179 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 605 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478779 none CN(CC1CCN(C(=O)C2=CNC(C#N)=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.1', 'N.1', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [32, 25, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 32, 60, 60, 100, 125, 179, 179, 179, 179, 179, 32, 32, 32, 25, 25, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 100, 100, 179] 179 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478779 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478779 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478779/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478779 Building REAL300025478780 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478780' /scratch/stefan/7787258/working/building/REAL300025478780 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478780 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478780/0 /scratch/stefan/7787258/working/building/REAL300025478780 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/673 `/scratch/stefan/7787258/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478780 none C#CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 51, 51, 15, 51, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 15, 19, 42, 42, 42, 42, 42, 1, 76, 76, 76, 51, 15, 15, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 15, 15, 42, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 372 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478780 none C#CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 196, 140, 196, 52, 42, 52, 42, 42, 42, 34, 29, 26, 29, 15, 26, 11, 1, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 196, 140, 140, 42, 42, 42, 42, 42, 34, 34, 29, 29, 29, 15, 15, 1, 42, 42] 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, 46, 47]) total number of confs: 769 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478780 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478780 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478780/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478780 Building REAL300025478781 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478781' /scratch/stefan/7787258/working/building/REAL300025478781 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478781 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478781/0 /scratch/stefan/7787258/working/building/REAL300025478781 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/674 `/scratch/stefan/7787258/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478781 none CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 9, 6, 9, 2, 1, 2, 1, 1, 1, 1, 1, 4, 5, 5, 7, 7, 14, 21, 64, 64, 64, 64, 64, 1, 18, 18, 18, 18, 18, 9, 6, 6, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 14, 14, 64, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478781 none CCNC(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 129, 128, 129, 84, 64, 84, 64, 64, 64, 64, 50, 39, 50, 28, 39, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 129, 128, 128, 64, 64, 64, 64, 64, 64, 64, 50, 50, 50, 28, 28, 1, 64, 64] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 982 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478781 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478781 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478781/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478781 Building REAL300025478782 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478782' /scratch/stefan/7787258/working/building/REAL300025478782 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478782 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478782/0 /scratch/stefan/7787258/working/building/REAL300025478782 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/675 `/scratch/stefan/7787258/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478782 none CNC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 24, 33, 14, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 16, 23, 63, 63, 63, 63, 63, 1, 33, 33, 33, 33, 22, 23, 17, 17, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 16, 16, 63, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 50, 51, 41, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 295 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478782 none CNC(=O)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 201, 146, 164, 70, 63, 70, 63, 63, 63, 54, 33, 28, 33, 21, 28, 11, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 170, 175, 176, 176, 164, 164, 63, 63, 63, 63, 63, 54, 54, 33, 33, 33, 21, 21, 1, 63, 63] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 991 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478782 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478782 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478782/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478782 Building REAL300025478783 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478783' /scratch/stefan/7787258/working/building/REAL300025478783 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478783 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478783/0 /scratch/stefan/7787258/working/building/REAL300025478783 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/676 `/scratch/stefan/7787258/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478783 none COC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 14, 22, 22, 43, 43, 74, 118, 201, 201, 201, 201, 201, 8, 1, 3, 3, 3, 8, 8, 8, 8, 8, 14, 14, 22, 22, 22, 74, 74, 201, 8, 8, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 511 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478783 none COC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 174, 201, 174, 174, 174, 160, 104, 64, 104, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 201, 174, 174, 174, 174, 174, 160, 160, 104, 104, 104, 28, 28, 1, 174, 174, 201] 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, 43, 44, 45]) total number of confs: 770 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478783 none COC1=NOC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 5, 12, 12, 31, 31, 59, 95, 174, 174, 174, 174, 174, 1, 7, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 59, 59, 174, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 439 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478783 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478783 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478783/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478783 Building REAL300025478784 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478784' /scratch/stefan/7787258/working/building/REAL300025478784 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478784 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478784/0 /scratch/stefan/7787258/working/building/REAL300025478784 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/677 `/scratch/stefan/7787258/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478784 none COC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 37, 18, 37, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 31, 42, 73, 73, 73, 73, 73, 1, 40, 40, 40, 37, 37, 37, 37, 20, 20, 14, 14, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 31, 31, 73, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 374 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478784 none COC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 181, 201, 169, 85, 73, 85, 73, 73, 73, 61, 42, 28, 42, 16, 28, 12, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 181, 181, 169, 169, 73, 73, 73, 73, 73, 61, 61, 42, 42, 42, 16, 16, 1, 73, 73] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 855 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478784 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478784 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478784/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478784 Building REAL300025478785 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478785' /scratch/stefan/7787258/working/building/REAL300025478785 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478785 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478785/0 /scratch/stefan/7787258/working/building/REAL300025478785 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/678 `/scratch/stefan/7787258/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1) `REAL300025478785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478785 none CCC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 13, 18, 18, 21, 21, 42, 59, 157, 157, 157, 157, 157, 6, 1, 1, 8, 8, 8, 7, 7, 6, 6, 6, 6, 6, 13, 13, 18, 18, 18, 42, 42, 157, 6, 6, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 47, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 377 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478785 none CCC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 157, 157, 156, 140, 156, 140, 140, 140, 124, 80, 55, 80, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 140, 157, 157, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 124, 124, 80, 80, 80, 30, 30, 1, 140, 140, 157] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 887 number of broken/clashed sets: 122 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478785 none CCC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 27, 43, 140, 140, 140, 140, 140, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 27, 27, 140, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 319 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478785 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478785 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478785/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478785 Building REAL300025478786 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478786' /scratch/stefan/7787258/working/building/REAL300025478786 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478786 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478786/0 /scratch/stefan/7787258/working/building/REAL300025478786 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/679 `/scratch/stefan/7787258/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478786 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 1, 15, 33, 33, 58, 85, 153, 153, 153, 153, 153, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 58, 58, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478786 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 66, 84, 132, 153, 153, 153, 153, 200, 200, 201, 201, 201, 201, 201, 201, 153, 33, 66, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 132, 132, 153, 153, 153, 153, 153, 201, 201, 201, 153, 153, 33, 33, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 805 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478786 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 32, 62, 62, 104, 141, 201, 201, 201, 201, 201, 32, 32, 32, 17, 17, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 104, 104, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 585 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478786 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478786 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478786/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478786 Building REAL300025478787 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478787' /scratch/stefan/7787258/working/building/REAL300025478787 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478787 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478787/0 /scratch/stefan/7787258/working/building/REAL300025478787 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/680 `/scratch/stefan/7787258/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=C(N)N(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478787 none CN(CC1CCN(C(=O)C2=C(N)N(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 1, 14, 30, 30, 55, 76, 128, 128, 128, 128, 128, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 55, 55, 128] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 356 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478787 none CN(CC1CCN(C(=O)C2=C(N)N(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 78, 84, 114, 128, 128, 128, 128, 156, 156, 201, 201, 201, 201, 201, 201, 128, 35, 78, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 114, 114, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 128, 128, 35, 35, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 689 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478787 none CN(CC1CCN(C(=O)C2=C(N)N(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 27, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 46, 70, 70, 110, 141, 201, 201, 201, 201, 201, 46, 46, 46, 27, 27, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 1, 10, 10, 110, 110, 201] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 620 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478787 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478787 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478787/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478787 Building REAL300025478788 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478788' /scratch/stefan/7787258/working/building/REAL300025478788 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478788 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478788/0 /scratch/stefan/7787258/working/building/REAL300025478788 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/681 `/scratch/stefan/7787258/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478788 none CN(CC1CCN(C(=O)C2=CN=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 3, 7, 7, 1, 13, 33, 33, 69, 95, 170, 170, 170, 170, 170, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 3, 7, 1, 1, 69, 69, 170] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 455 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478788 none CN(CC1CCN(C(=O)C2=CN=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 73, 95, 146, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 170, 38, 73, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 146, 146, 170, 170, 170, 170, 170, 201, 201, 201, 170, 170, 38, 38, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 798 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478788 none CN(CC1CCN(C(=O)C2=CN=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 20, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 41, 66, 66, 91, 124, 201, 201, 201, 201, 201, 41, 41, 41, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 91, 91, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 545 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478788 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478788 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478788/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478788 Building REAL300025478789 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478789' /scratch/stefan/7787258/working/building/REAL300025478789 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478789 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478789/0 /scratch/stefan/7787258/working/building/REAL300025478789 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/682 `/scratch/stefan/7787258/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 13, 33, 33, 68, 91, 148, 148, 148, 148, 148, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 10, 1, 1, 68, 68, 148] 402 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 429 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [79, 60, 79, 130, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 148, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 130, 130, 148, 148, 148, 148, 148, 201, 201, 201, 402, 148, 148, 31, 31, 1] 402 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1220 number of broken/clashed sets: 136 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [31, 15, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 31, 61, 61, 107, 142, 201, 201, 201, 201, 201, 31, 31, 31, 15, 15, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 107, 107, 201] 402 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 606 number of broken/clashed sets: 136 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478789 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478789/1 /scratch/stefan/7787258/working/building/REAL300025478789 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/683 `/scratch/stefan/7787258/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NC=CC=C2[O-])C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478789.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 1, 13, 28, 28, 37, 54, 105, 105, 105, 105, 105, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 37, 37, 105] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 262 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: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 68, 76, 92, 105, 105, 105, 105, 172, 172, 201, 201, 201, 201, 201, 201, 105, 34, 68, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 92, 92, 105, 105, 105, 105, 105, 201, 201, 201, 105, 105, 34, 34, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 722 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: REAL300025478789 none CN(CC1CCN(C(=O)C2=NC=CC=C2[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 24, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 41, 78, 78, 95, 131, 201, 201, 201, 201, 201, 41, 41, 41, 24, 24, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 95, 95, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 547 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478789 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478789 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478789/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478789/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478789 Building REAL300025478790 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478790' /scratch/stefan/7787258/working/building/REAL300025478790 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478790 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478790/0 /scratch/stefan/7787258/working/building/REAL300025478790 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/684 `/scratch/stefan/7787258/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478790 none CN(CC1CCN(C(=O)C2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 1, 14, 31, 31, 62, 86, 172, 172, 172, 172, 172, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 62, 62, 172] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 434 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: REAL300025478790 none CN(CC1CCN(C(=O)C2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 79, 97, 153, 172, 172, 172, 172, 198, 198, 201, 201, 201, 201, 201, 172, 37, 79, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 153, 153, 172, 172, 172, 172, 172, 201, 201, 201, 201, 201, 201, 201, 172, 172, 37, 37, 1] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 801 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: REAL300025478790 none CN(CC1CCN(C(=O)C2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 24, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 41, 73, 73, 110, 138, 201, 201, 201, 201, 201, 41, 41, 41, 24, 24, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 110, 110, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 596 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478790 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478790 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478790/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478790 Building REAL300025478791 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478791' /scratch/stefan/7787258/working/building/REAL300025478791 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478791 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478791/0 /scratch/stefan/7787258/working/building/REAL300025478791 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/685 `/scratch/stefan/7787258/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478791 none CN(CC1CCN(C(=O)CC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 17, 45, 45, 45, 45, 1, 9, 12, 12, 20, 20, 46, 46, 46, 46, 46, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 45, 45, 45, 1, 1, 20, 20, 46] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 217 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: REAL300025478791 none CN(CC1CCN(C(=O)CC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 41, 46, 46, 46, 46, 53, 53, 110, 201, 201, 201, 201, 46, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 41, 41, 46, 46, 46, 46, 46, 110, 110, 201, 201, 201, 46, 46, 29, 29, 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: 607 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: REAL300025478791 none CN(CC1CCN(C(=O)CC2=COC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 73, 45, 45, 45, 45, 19, 5, 19, 1, 1, 1, 1, 1, 1, 45, 107, 130, 130, 153, 153, 201, 201, 201, 201, 201, 107, 107, 107, 73, 73, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 45, 45, 153, 153, 201] 201 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 674 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478791 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478791 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478791/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478791 Building REAL300025478792 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478792' /scratch/stefan/7787258/working/building/REAL300025478792 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478792 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478792/0 /scratch/stefan/7787258/working/building/REAL300025478792 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/686 `/scratch/stefan/7787258/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1) `REAL300025478792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478792 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 18, 31, 31, 50, 50, 75, 120, 201, 201, 201, 201, 201, 6, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 18, 18, 31, 31, 31, 75, 75, 201, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 44, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 522 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: REAL300025478792 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 180, 201, 180, 180, 180, 162, 104, 64, 104, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 162, 162, 104, 104, 104, 30, 30, 1, 180, 180, 201] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 781 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: REAL300025478792 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 14, 14, 34, 34, 59, 94, 180, 180, 180, 180, 180, 1, 6, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 59, 59, 180, 1, 1, 7] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 43, 42, 23, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 433 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478792 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478792 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478792/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478792 Building REAL300025478793 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478793' /scratch/stefan/7787258/working/building/REAL300025478793 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478793 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478793/0 /scratch/stefan/7787258/working/building/REAL300025478793 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/687 `/scratch/stefan/7787258/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478793 none CN(CC1CCN(C(=O)C2=CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 1, 13, 30, 30, 62, 84, 153, 153, 153, 153, 153, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 62, 62, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 415 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478793 none CN(CC1CCN(C(=O)C2=CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 69, 86, 130, 153, 153, 153, 153, 165, 165, 201, 201, 201, 201, 201, 201, 153, 35, 69, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 130, 130, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 35, 35, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 749 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478793 none CN(CC1CCN(C(=O)C2=CCCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 34, 67, 67, 112, 138, 201, 201, 201, 201, 201, 34, 34, 34, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 112, 112, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 624 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478793 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478793 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478793/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478793 Building REAL300025478794 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478794' /scratch/stefan/7787258/working/building/REAL300025478794 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478794 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478794/0 /scratch/stefan/7787258/working/building/REAL300025478794 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/688 `/scratch/stefan/7787258/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478794 none C[C@H](NC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 6, 6, 11, 11, 11, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 16, 16, 38, 64, 147, 147, 147, 147, 147, 1, 6, 6, 6, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 38, 38, 147, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 372 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478794 none C[C@H](NC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 201, 201, 201, 201, 201, 147, 178, 147, 147, 147, 138, 99, 66, 99, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 138, 138, 99, 99, 99, 30, 30, 1, 147, 147] 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, 46, 47]) total number of confs: 811 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478794 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478794 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478794/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478794 Building REAL300025478795 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478795' /scratch/stefan/7787258/working/building/REAL300025478795 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478795 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478795/0 /scratch/stefan/7787258/working/building/REAL300025478795 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/689 `/scratch/stefan/7787258/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2OCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478795 none CN(CC1CCN(C(=O)CC2OCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 22, 43, 43, 43, 43, 43, 1, 10, 15, 15, 23, 24, 57, 57, 57, 57, 57, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 22, 22, 43, 43, 43, 43, 43, 43, 43, 1, 1, 23, 23, 57] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 278 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478795 none CN(CC1CCN(C(=O)CC2OCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 46, 50, 57, 57, 57, 57, 81, 81, 180, 201, 201, 201, 201, 201, 57, 33, 44, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 50, 50, 57, 57, 57, 57, 57, 180, 180, 201, 201, 201, 201, 201, 201, 201, 57, 57, 33, 33, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 828 number of broken/clashed sets: 108 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478795 none CN(CC1CCN(C(=O)CC2OCCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 75, 43, 43, 43, 43, 22, 8, 22, 1, 1, 1, 1, 1, 1, 1, 43, 102, 135, 135, 155, 155, 201, 201, 201, 201, 201, 102, 102, 102, 75, 75, 43, 43, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 43, 43, 155, 155, 201] 201 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50]) total number of confs: 661 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478795 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478795 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478795/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478795 Building REAL300025478796 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478796' /scratch/stefan/7787258/working/building/REAL300025478796 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478796 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478796/0 /scratch/stefan/7787258/working/building/REAL300025478796 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/690 `/scratch/stefan/7787258/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1) `REAL300025478796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478796 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 25, 38, 38, 45, 45, 74, 108, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 25, 25, 38, 38, 38, 74, 74, 201, 10, 10, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 550 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478796 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 131, 153, 131, 131, 131, 116, 80, 53, 80, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 116, 116, 80, 80, 80, 29, 29, 1, 131, 131, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 697 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478796 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 38, 57, 131, 131, 131, 131, 131, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 38, 38, 131, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 322 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478796 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478796 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478796/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478796 Building REAL300025478797 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478797' /scratch/stefan/7787258/working/building/REAL300025478797 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478797 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478797/0 /scratch/stefan/7787258/working/building/REAL300025478797 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/691 `/scratch/stefan/7787258/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C=CC2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478797 none CN(CC1CCN(C(=O)C=CC2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 14, 14, 14, 14, 1, 5, 6, 6, 7, 7, 13, 13, 13, 13, 13, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 1, 1, 7, 7, 13] 21 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 64 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: REAL300025478797 none CN(CC1CCN(C(=O)C=CC2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 19, 19, 21, 21, 21, 21, 13, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 19, 19, 21, 21, 21, 21, 13, 13, 12, 12, 1] 21 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 50 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: REAL300025478797 none CN(CC1CCN(C(=O)C=CC2=CC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 14, 14, 14, 14, 13, 6, 13, 6, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 20, 20, 21, 21, 21, 21, 21, 19, 19, 19, 18, 18, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 14, 14, 20, 20, 21] 21 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478797 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478797 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478797/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478797 Building REAL300025478798 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478798' /scratch/stefan/7787258/working/building/REAL300025478798 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478798 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478798/0 /scratch/stefan/7787258/working/building/REAL300025478798 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/692 `/scratch/stefan/7787258/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=C1) `REAL300025478798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478798 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 21, 32, 32, 54, 54, 77, 119, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 21, 21, 32, 32, 32, 77, 77, 201, 7, 7, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 49, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 541 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: REAL300025478798 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 114, 143, 114, 114, 114, 99, 66, 48, 66, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 201, 201, 114, 114, 114, 114, 114, 99, 99, 66, 66, 66, 26, 26, 1, 114, 114, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 662 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: REAL300025478798 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 5, 10, 10, 23, 23, 40, 61, 114, 114, 114, 114, 114, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 40, 40, 114, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 303 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478798 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478798 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478798/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478798 Building REAL300025478799 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478799' /scratch/stefan/7787258/working/building/REAL300025478799 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478799 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478799/0 /scratch/stefan/7787258/working/building/REAL300025478799 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/693 `/scratch/stefan/7787258/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN=N1) `REAL300025478799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478799 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 27, 37, 37, 45, 45, 74, 115, 201, 201, 201, 201, 201, 12, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 12, 12, 27, 27, 37, 37, 37, 74, 74, 201, 12, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 538 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478799 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 156, 145, 156, 145, 145, 145, 127, 88, 62, 88, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 127, 127, 88, 88, 88, 29, 29, 1, 145, 145, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 675 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478799 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 42, 66, 145, 145, 145, 145, 145, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 42, 42, 145, 1, 1, 12] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 355 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478799 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478799 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478799/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478799 Building REAL300025478800 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478800' /scratch/stefan/7787258/working/building/REAL300025478800 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478800 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478800/0 /scratch/stefan/7787258/working/building/REAL300025478800 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/694 `/scratch/stefan/7787258/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCN2C=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478800 none CN(CC1CCN(C(=O)CCN2C=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 28, 52, 52, 52, 52, 1, 10, 15, 15, 23, 24, 55, 55, 55, 55, 55, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 18, 18, 28, 28, 52, 52, 1, 1, 23, 23, 55] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 286 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478800 none CN(CC1CCN(C(=O)CCN2C=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 46, 51, 55, 55, 55, 55, 77, 77, 171, 186, 201, 201, 201, 201, 55, 32, 44, 13, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 51, 51, 55, 55, 55, 55, 55, 171, 171, 186, 186, 201, 201, 55, 55, 32, 32, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 809 number of broken/clashed sets: 103 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478800 none CN(CC1CCN(C(=O)CCN2C=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 84, 52, 52, 52, 52, 34, 14, 34, 8, 1, 1, 1, 1, 1, 1, 52, 111, 139, 139, 157, 157, 201, 201, 201, 201, 201, 111, 111, 111, 84, 84, 52, 52, 52, 52, 52, 14, 14, 8, 8, 1, 1, 52, 52, 157, 157, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 675 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478800 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478800 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478800/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478800 Building REAL300025478801 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478801' /scratch/stefan/7787258/working/building/REAL300025478801 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478801 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478801/0 /scratch/stefan/7787258/working/building/REAL300025478801 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/695 `/scratch/stefan/7787258/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478801 none CC(=O)N1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 26, 36, 36, 37, 37, 56, 86, 170, 170, 170, 170, 170, 10, 1, 3, 3, 3, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 36, 36, 36, 56, 56, 170, 10, 10, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 48, 49, 26, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478801 none CC(=O)N1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 201, 170, 170, 106, 95, 106, 95, 95, 95, 80, 65, 47, 65, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 95, 170, 201, 201, 201, 170, 170, 170, 95, 95, 95, 95, 95, 80, 80, 65, 65, 65, 27, 27, 1, 95, 95, 170, 170] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 749 number of broken/clashed sets: 103 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478801 none CC(=O)N1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 17, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 21, 35, 95, 95, 95, 95, 95, 1, 10, 17, 17, 17, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 21, 21, 95, 1, 1, 10, 10] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 251 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478801 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478801 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478801/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478801 Building REAL300025478802 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478802' /scratch/stefan/7787258/working/building/REAL300025478802 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478802 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478802/0 /scratch/stefan/7787258/working/building/REAL300025478802 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/696 `/scratch/stefan/7787258/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(=O)N(C)O2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478802 none CN(CC1CCN(C(=O)C2=CC(=O)N(C)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 1, 13, 27, 27, 60, 84, 167, 167, 167, 167, 167, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 60, 60, 167] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 424 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478802 none CN(CC1CCN(C(=O)C2=CC(=O)N(C)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 87, 98, 148, 167, 167, 167, 167, 190, 190, 201, 201, 201, 201, 201, 201, 167, 40, 87, 13, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 148, 148, 167, 167, 167, 167, 167, 201, 201, 201, 201, 167, 167, 40, 40, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 777 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478802 none CN(CC1CCN(C(=O)C2=CC(=O)N(C)O2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 22, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 35, 58, 58, 104, 134, 201, 201, 201, 201, 201, 35, 35, 35, 22, 22, 10, 10, 10, 10, 10, 1, 2, 2, 2, 10, 10, 104, 104, 201] 201 rigid atoms, others: [37, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 598 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478802 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478802 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478802/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478802 Building REAL300025478803 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478803' /scratch/stefan/7787258/working/building/REAL300025478803 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478803 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478803/0 /scratch/stefan/7787258/working/building/REAL300025478803 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/697 `/scratch/stefan/7787258/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478803 none CCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 20, 31, 95, 95, 95, 95, 95, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 13, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 20, 20, 95, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 281 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478803 none CCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 201, 95, 95, 95, 95, 95, 95, 79, 50, 39, 50, 26, 39, 13, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 95, 95, 95, 95, 95, 79, 79, 50, 50, 50, 26, 26, 1, 95, 95] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 889 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478803 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478803 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478803/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478803 Building REAL300025478804 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478804' /scratch/stefan/7787258/working/building/REAL300025478804 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478804 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478804/0 /scratch/stefan/7787258/working/building/REAL300025478804 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/698 `/scratch/stefan/7787258/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478804 none COC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 6, 12, 12, 19, 19, 19, 19, 31, 36, 36, 37, 37, 75, 113, 201, 201, 201, 201, 201, 19, 1, 1, 1, 5, 5, 5, 6, 6, 19, 19, 19, 19, 19, 31, 31, 36, 36, 36, 75, 75, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 546 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478804 none COC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 119, 117, 119, 117, 117, 117, 91, 65, 51, 65, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 201, 192, 192, 117, 117, 117, 117, 117, 91, 91, 65, 65, 65, 29, 29, 1, 117, 117, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 846 number of broken/clashed sets: 143 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478804 none COC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 13, 4, 1, 4, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 23, 36, 117, 117, 117, 117, 117, 1, 19, 19, 19, 24, 24, 24, 13, 13, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 117, 1, 1, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 305 number of broken/clashed sets: 143 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478804 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478804 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478804/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478804 Building REAL300025478805 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478805' /scratch/stefan/7787258/working/building/REAL300025478805 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478805 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478805/0 /scratch/stefan/7787258/working/building/REAL300025478805 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/699 `/scratch/stefan/7787258/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478805 none CC1OCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 17, 30, 30, 52, 52, 81, 130, 201, 201, 201, 201, 201, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 30, 30, 30, 81, 81, 201, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 561 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: REAL300025478805 none CC1OCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 179, 201, 179, 179, 179, 155, 97, 62, 97, 27, 62, 12, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 155, 155, 97, 97, 97, 27, 27, 1, 179, 179] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 775 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: REAL300025478805 none CC1OCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 29, 29, 55, 90, 179, 179, 179, 179, 179, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 55, 55, 179, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 431 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478805 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478805 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478805/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478805 Building REAL300025478806 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478806' /scratch/stefan/7787258/working/building/REAL300025478806 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478806 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478806/0 /scratch/stefan/7787258/working/building/REAL300025478806 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/700 `/scratch/stefan/7787258/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478806 none C#CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 15, 24, 59, 59, 59, 59, 59, 1, 28, 27, 27, 18, 18, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 15, 15, 59, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 273 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478806 none C#CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 123, 59, 59, 59, 59, 59, 59, 52, 32, 30, 32, 24, 30, 12, 1, 1, 1, 1, 1, 1, 1, 59, 201, 199, 201, 145, 145, 123, 123, 59, 59, 59, 59, 59, 52, 52, 32, 32, 32, 24, 24, 1, 59, 59] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 980 number of broken/clashed sets: 154 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478806 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478806 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478806/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478806 Building REAL300025478807 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478807' /scratch/stefan/7787258/working/building/REAL300025478807 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478807 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478807/0 /scratch/stefan/7787258/working/building/REAL300025478807 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/701 `/scratch/stefan/7787258/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=C(Cl)OC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478807 none CN(CC1CCN(C(=O)C2=C(Cl)OC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 14, 31, 31, 61, 89, 157, 157, 157, 157, 157, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 9, 9, 1, 1, 61, 61, 157] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 15, 35, 38, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 40, 41, 42]) total number of confs: 410 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478807 none CN(CC1CCN(C(=O)C2=C(Cl)OC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 82, 99, 143, 157, 157, 157, 157, 177, 177, 201, 201, 201, 201, 201, 157, 41, 82, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 143, 143, 157, 157, 157, 157, 157, 201, 201, 157, 157, 41, 41, 1] 201 rigid atoms, others: [42, 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: 745 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478807 none CN(CC1CCN(C(=O)C2=C(Cl)OC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 43, 73, 73, 113, 146, 201, 201, 201, 201, 201, 43, 43, 43, 24, 24, 9, 9, 9, 9, 9, 1, 1, 9, 9, 113, 113, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 606 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478807 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478807 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478807/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478807 Building REAL300025478808 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478808' /scratch/stefan/7787258/working/building/REAL300025478808 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478808 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478808/0 /scratch/stefan/7787258/working/building/REAL300025478808 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/702 `/scratch/stefan/7787258/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478808 none C=CC(C)(O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 39, 68, 183, 183, 183, 183, 183, 1, 10, 10, 10, 7, 7, 7, 21, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 39, 39, 183, 1, 1] 603 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 433 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478808 none C=CC(C)(O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 196, 183, 196, 183, 183, 183, 166, 114, 75, 114, 29, 75, 13, 1, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 201, 603, 201, 201, 183, 183, 183, 183, 183, 166, 166, 114, 114, 114, 29, 29, 1, 183, 183] 603 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 1364 number of broken/clashed sets: 294 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478808 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478808 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478808/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478808 Building REAL300025478809 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478809' /scratch/stefan/7787258/working/building/REAL300025478809 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478809 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478809/0 /scratch/stefan/7787258/working/building/REAL300025478809 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/703 `/scratch/stefan/7787258/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1) `REAL300025478809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478809 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 21, 29, 29, 48, 48, 82, 119, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 21, 21, 29, 29, 29, 82, 82, 201, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 560 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: REAL300025478809 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 175, 113, 175, 113, 113, 113, 107, 79, 57, 79, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 113, 113, 113, 113, 113, 107, 107, 79, 79, 79, 27, 27, 1, 113, 113] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 699 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: REAL300025478809 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 5, 10, 10, 19, 19, 36, 54, 113, 113, 113, 113, 113, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 36, 36, 113, 1, 1] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 288 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478809 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478809 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478809/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478809 Building REAL300025478810 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478810' /scratch/stefan/7787258/working/building/REAL300025478810 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478810 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478810/0 /scratch/stefan/7787258/working/building/REAL300025478810 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/704 `/scratch/stefan/7787258/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478810 none CCN1C=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 16, 21, 21, 27, 27, 44, 70, 125, 125, 125, 125, 125, 6, 3, 3, 3, 3, 3, 1, 1, 6, 6, 6, 6, 6, 16, 16, 21, 21, 21, 44, 44, 125, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 332 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: REAL300025478810 none CCN1C=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 125, 125, 116, 86, 116, 86, 86, 86, 78, 63, 51, 63, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 125, 125, 86, 86, 86, 86, 86, 78, 78, 63, 63, 63, 27, 27, 1, 86, 86] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 909 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: REAL300025478810 none CCN1C=CN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 24, 36, 86, 86, 86, 86, 86, 1, 11, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 24, 24, 86, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478810 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478810 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478810/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478810 Building REAL300025478811 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478811' /scratch/stefan/7787258/working/building/REAL300025478811 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478811 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478811/0 /scratch/stefan/7787258/working/building/REAL300025478811 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/705 `/scratch/stefan/7787258/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478811 none CN(CC1CCN(C(=O)C2CCCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 1, 13, 31, 31, 60, 83, 133, 133, 133, 133, 133, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 60, 60, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 371 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478811 none CN(CC1CCN(C(=O)C2CCCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 73, 89, 117, 133, 133, 133, 133, 137, 137, 201, 201, 201, 201, 201, 201, 133, 39, 73, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 117, 117, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 39, 39, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 798 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478811 none CN(CC1CCN(C(=O)C2CCCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 29, 62, 62, 103, 140, 201, 201, 201, 201, 201, 29, 29, 29, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 103, 103, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 577 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478811 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478811 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478811/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478811 Building REAL300025478812 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478812' /scratch/stefan/7787258/working/building/REAL300025478812 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478812 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478812/0 /scratch/stefan/7787258/working/building/REAL300025478812 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/706 `/scratch/stefan/7787258/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=NC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478812 none CN(CC1CCN(C(=O)CCC2=NC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 4, 4, 8, 10, 11, 11, 11, 11, 1, 7, 9, 9, 11, 11, 28, 28, 28, 28, 28, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 8, 8, 10, 10, 11, 11, 11, 1, 1, 11, 11, 28] 49 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 100 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: REAL300025478812 none CN(CC1CCN(C(=O)CCC2=NC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 28, 28, 28, 28, 35, 35, 47, 49, 49, 49, 49, 49, 28, 24, 26, 11, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 47, 47, 49, 49, 49, 49, 49, 28, 28, 24, 24, 1] 49 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 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: REAL300025478812 none CN(CC1CCN(C(=O)CCC2=NC=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [37, 28, 18, 18, 18, 18, 13, 8, 13, 6, 1, 1, 1, 1, 1, 1, 18, 37, 49, 49, 50, 50, 73, 73, 73, 73, 73, 37, 37, 37, 28, 28, 18, 18, 18, 18, 18, 8, 8, 6, 6, 1, 1, 1, 18, 18, 50, 50, 73] 73 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 233 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478812 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478812 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478812/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478812 Building REAL300025478813 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478813' /scratch/stefan/7787258/working/building/REAL300025478813 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478813 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478813/0 /scratch/stefan/7787258/working/building/REAL300025478813 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/707 `/scratch/stefan/7787258/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC(O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478813 none CN(CC1CCN(C(=O)C2CCC(O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 11, 29, 29, 57, 80, 135, 135, 135, 135, 135, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 18, 6, 6, 6, 6, 1, 1, 57, 57, 135] 603 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 390 number of broken/clashed sets: 282 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478813 none CN(CC1CCN(C(=O)C2CCC(O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 71, 86, 117, 135, 135, 135, 135, 139, 139, 201, 201, 201, 201, 201, 201, 135, 37, 71, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 117, 117, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 201, 135, 135, 37, 37, 1] 603 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 1403 number of broken/clashed sets: 282 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478813 none CN(CC1CCN(C(=O)C2CCC(O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 26, 57, 57, 98, 136, 201, 201, 201, 201, 201, 26, 26, 26, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 6, 6, 98, 98, 201] 603 rigid atoms, others: [45, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 48, 49, 50, 51, 52]) total number of confs: 579 number of broken/clashed sets: 282 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478813 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478813 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478813/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478813 Building REAL300025478814 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478814' /scratch/stefan/7787258/working/building/REAL300025478814 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478814 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478814/0 /scratch/stefan/7787258/working/building/REAL300025478814 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/708 `/scratch/stefan/7787258/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(C)(C)O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478814 none CN(CC1CCN(C(=O)CC(C)(C)O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 11, 11, 11, 1, 8, 10, 10, 13, 13, 25, 25, 25, 25, 25, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 33, 1, 1, 13, 13, 25] 102 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478814 none CN(CC1CCN(C(=O)CC(C)(C)O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 23, 25, 25, 25, 25, 25, 25, 32, 34, 34, 34, 25, 21, 22, 11, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 32, 32, 34, 34, 34, 34, 34, 34, 102, 25, 25, 21, 21, 1] 102 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478814 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478814 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478814/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478814 Building REAL300025478815 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478815' /scratch/stefan/7787258/working/building/REAL300025478815 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478815 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478815/0 /scratch/stefan/7787258/working/building/REAL300025478815 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/709 `/scratch/stefan/7787258/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478815 none CC1=CC=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 33, 43, 43, 47, 47, 74, 114, 201, 201, 201, 201, 201, 16, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 33, 33, 43, 43, 43, 74, 74, 201, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 530 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478815 none CC1=CC=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 118, 111, 118, 111, 111, 111, 92, 70, 49, 70, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 92, 92, 70, 70, 70, 27, 27, 1, 111, 111] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 604 number of broken/clashed sets: 85 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478815 none CC1=CC=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 23, 35, 111, 111, 111, 111, 111, 1, 16, 17, 17, 17, 16, 17, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 111, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478815 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478815 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478815/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478815 Building REAL300025478816 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478816' /scratch/stefan/7787258/working/building/REAL300025478816 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478816 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478816/0 /scratch/stefan/7787258/working/building/REAL300025478816 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/710 `/scratch/stefan/7787258/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478816 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 29, 48, 132, 132, 132, 132, 132, 1, 9, 14, 14, 11, 11, 11, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 29, 29, 132, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 328 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478816 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 5, 10, 10, 14, 14, 14, 14, 28, 36, 36, 42, 42, 76, 118, 201, 201, 201, 201, 201, 14, 1, 1, 1, 9, 9, 9, 5, 14, 14, 14, 14, 14, 28, 28, 36, 36, 36, 76, 76, 201, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 564 number of broken/clashed sets: 126 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478816 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 164, 132, 164, 132, 132, 132, 110, 69, 48, 69, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 132, 189, 201, 201, 189, 189, 189, 189, 132, 132, 132, 132, 132, 110, 110, 69, 69, 69, 28, 28, 1, 132, 132, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 827 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478816 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478816 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478816/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478816 Building REAL300025478817 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478817' /scratch/stefan/7787258/working/building/REAL300025478817 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478817 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478817/0 /scratch/stefan/7787258/working/building/REAL300025478817 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/711 `/scratch/stefan/7787258/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1) `REAL300025478817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478817 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 13, 18, 18, 20, 20, 43, 66, 134, 134, 134, 134, 134, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 18, 18, 18, 43, 43, 134, 6, 6, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478817 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 107, 86, 107, 86, 86, 86, 70, 47, 34, 47, 22, 34, 13, 1, 1, 1, 1, 1, 1, 1, 86, 134, 134, 134, 201, 201, 201, 201, 201, 86, 86, 86, 86, 86, 70, 70, 47, 47, 47, 22, 22, 1, 86, 86, 134, 134] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 864 number of broken/clashed sets: 122 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478817 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 23, 36, 86, 86, 86, 86, 86, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 86, 1, 1, 6, 6] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 252 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478817 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478817 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478817/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478817 Building REAL300025478818 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478818' /scratch/stefan/7787258/working/building/REAL300025478818 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478818 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478818/0 /scratch/stefan/7787258/working/building/REAL300025478818 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/712 `/scratch/stefan/7787258/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=C1) `REAL300025478818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478818 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 30, 40, 40, 50, 50, 77, 120, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 30, 30, 40, 40, 40, 77, 77, 201, 11, 11, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478818 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 137, 155, 137, 137, 137, 122, 86, 62, 86, 28, 62, 12, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 122, 122, 86, 86, 86, 28, 28, 1, 137, 137, 201, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 688 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478818 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 40, 64, 137, 137, 137, 137, 137, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 40, 40, 137, 1, 1, 11, 11, 11] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 337 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478818 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478818 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478818/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478818 Building REAL300025478819 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478819' /scratch/stefan/7787258/working/building/REAL300025478819 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478819 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478819/0 /scratch/stefan/7787258/working/building/REAL300025478819 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/713 `/scratch/stefan/7787258/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478819 none CN(CC1CCN(C(=O)C2=CN=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 12, 22, 22, 47, 66, 123, 123, 123, 123, 123, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 47, 47, 123] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478819 none CN(CC1CCN(C(=O)C2=CN=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 65, 75, 109, 123, 123, 123, 123, 172, 172, 201, 201, 201, 201, 201, 123, 34, 65, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 109, 109, 123, 123, 123, 123, 123, 201, 201, 201, 201, 123, 123, 34, 34, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 759 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478819 none CN(CC1CCN(C(=O)C2=CN=NN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 21, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 40, 63, 63, 108, 139, 201, 201, 201, 201, 201, 40, 40, 40, 21, 21, 9, 9, 9, 9, 9, 1, 2, 2, 2, 9, 9, 108, 108, 201] 201 rigid atoms, others: [36, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 603 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478819 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478819 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478819/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478819 Building REAL300025478820 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478820' /scratch/stefan/7787258/working/building/REAL300025478820 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478820 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478820/0 /scratch/stefan/7787258/working/building/REAL300025478820 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/714 `/scratch/stefan/7787258/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2COC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478820 none CN(CC1CCN(C(=O)C2COC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 1, 1, 1, 1, 1, 1, 4, 5, 10, 10, 10, 10, 10, 1, 16, 26, 26, 47, 65, 104, 104, 104, 104, 104, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 47, 47, 104] 121 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 299 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: REAL300025478820 none CN(CC1CCN(C(=O)C2COC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [68, 64, 68, 94, 104, 104, 104, 104, 107, 107, 121, 121, 121, 121, 121, 104, 38, 64, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 94, 94, 104, 104, 104, 104, 104, 121, 121, 121, 121, 104, 104, 38, 38, 1] 121 rigid atoms, others: [44, 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]) total number of confs: 479 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: REAL300025478820 none CN(CC1CCN(C(=O)C2COC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [30, 16, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 30, 44, 44, 68, 87, 121, 121, 121, 121, 121, 30, 30, 30, 16, 16, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 68, 68, 121] 121 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478820 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478820 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478820/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478820 Building REAL300025478821 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478821' /scratch/stefan/7787258/working/building/REAL300025478821 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478821 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478821/0 /scratch/stefan/7787258/working/building/REAL300025478821 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/715 `/scratch/stefan/7787258/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478821 none CCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 25, 42, 85, 85, 85, 85, 85, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 25, 25, 85, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478821 none CCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 164, 90, 164, 85, 90, 85, 85, 85, 72, 57, 39, 57, 22, 39, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 85, 85, 85, 85, 85, 72, 72, 57, 57, 57, 22, 22, 1, 85, 85] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 927 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478821 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478821 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478821/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478821 Building REAL300025478822 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478822' /scratch/stefan/7787258/working/building/REAL300025478822 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478822 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478822/0 /scratch/stefan/7787258/working/building/REAL300025478822 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/716 `/scratch/stefan/7787258/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478822 none CC1CC(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 10, 20, 20, 43, 43, 76, 121, 201, 201, 201, 201, 201, 3, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 76, 76, 201, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 26, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 521 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: REAL300025478822 none CC1CC(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 190, 201, 190, 190, 190, 172, 122, 78, 122, 29, 78, 12, 1, 1, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 190, 190, 172, 172, 122, 122, 122, 29, 29, 1, 190, 190] 201 rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 740 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: REAL300025478822 none CC1CC(C)C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 15, 15, 37, 37, 70, 113, 190, 190, 190, 190, 190, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 70, 70, 190, 1, 1] 201 rigid atoms, others: [6, 38, 39, 8, 9, 10, 11, 12, 40, 51, 52, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 480 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478822 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478822 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478822/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478822 Building REAL300025478823 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478823' /scratch/stefan/7787258/working/building/REAL300025478823 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478823 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478823/0 /scratch/stefan/7787258/working/building/REAL300025478823 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/717 `/scratch/stefan/7787258/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2C[C@@H]2C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478823 none CN(CC1CCN(C(=O)[C@H]2C[C@@H]2C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 22, 22, 1, 8, 9, 9, 12, 12, 19, 19, 19, 19, 19, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 13, 13, 22, 1, 1, 12, 12, 19] 40 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478823 none CN(CC1CCN(C(=O)[C@H]2C[C@@H]2C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 24, 24, 40, 40, 40, 40, 40, 40, 40, 19, 17, 19, 12, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 40, 40, 40, 19, 19, 17, 17, 1] 40 rigid atoms, others: [45, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478823 none CN(CC1CCN(C(=O)[C@H]2C[C@@H]2C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 13, 23, 26, 26, 30, 30, 40, 40, 40, 40, 40, 23, 23, 23, 18, 18, 13, 13, 13, 13, 13, 1, 1, 8, 13, 13, 30, 30, 40] 40 rigid atoms, others: [38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 149 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478823 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478823 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478823/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478823 Building REAL300025478824 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478824' /scratch/stefan/7787258/working/building/REAL300025478824 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478824 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478824/0 /scratch/stefan/7787258/working/building/REAL300025478824 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/718 `/scratch/stefan/7787258/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478824 none CC1=COC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 19, 32, 32, 56, 56, 80, 123, 201, 201, 201, 201, 201, 5, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 5, 19, 19, 32, 32, 32, 80, 80, 201, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 554 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478824 none CC1=COC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 126, 103, 126, 103, 103, 103, 96, 65, 49, 65, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 96, 96, 65, 65, 65, 25, 25, 1, 103, 103] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 635 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478824 none CC1=COC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 37, 58, 103, 103, 103, 103, 103, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 37, 37, 103, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 285 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478824 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478824 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478824/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478824 Building REAL300025478825 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478825' /scratch/stefan/7787258/working/building/REAL300025478825 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478825 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478825/0 /scratch/stefan/7787258/working/building/REAL300025478825 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/719 `/scratch/stefan/7787258/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478825 none CN(CC1CCN(C(=O)C2CC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 1, 11, 26, 26, 48, 62, 112, 112, 112, 112, 112, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 48, 48, 112] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 327 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478825 none CN(CC1CCN(C(=O)C2CC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 62, 68, 100, 112, 112, 112, 112, 116, 116, 201, 201, 201, 201, 201, 112, 35, 62, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 100, 100, 112, 112, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 35, 35, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 804 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478825 none CN(CC1CCN(C(=O)C2CC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 33, 65, 65, 103, 129, 201, 201, 201, 201, 201, 33, 33, 33, 21, 21, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 10, 10, 103, 103, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 623 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478825 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478825 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478825/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478825 Building REAL300025478826 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478826' /scratch/stefan/7787258/working/building/REAL300025478826 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478826 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478826/0 /scratch/stefan/7787258/working/building/REAL300025478826 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/720 `/scratch/stefan/7787258/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1) `REAL300025478826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478826 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 17, 25, 25, 29, 29, 52, 73, 124, 124, 124, 124, 124, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 17, 17, 25, 25, 25, 52, 52, 124, 7, 7, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 49, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478826 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 107, 89, 107, 89, 89, 89, 74, 56, 44, 56, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 89, 124, 124, 124, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 74, 74, 56, 56, 56, 27, 27, 1, 89, 89, 124, 124, 124] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 893 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478826 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 14, 14, 29, 42, 89, 89, 89, 89, 89, 1, 7, 7, 7, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 29, 29, 89, 1, 1, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478826 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478826 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478826/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478826 Building REAL300025478827 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478827' /scratch/stefan/7787258/working/building/REAL300025478827 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478827 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478827/0 /scratch/stefan/7787258/working/building/REAL300025478827 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/721 `/scratch/stefan/7787258/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478827 none CC(C)[C@@H](O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 8, 11, 3, 8, 8, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 35, 56, 131, 131, 131, 131, 131, 1, 11, 11, 11, 11, 11, 11, 11, 24, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 35, 35, 131, 1, 1] 603 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 359 number of broken/clashed sets: 318 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478827 none CC(C)[C@@H](O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 193, 201, 141, 193, 193, 131, 141, 131, 131, 131, 116, 86, 58, 86, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 579, 131, 131, 131, 131, 131, 116, 116, 86, 86, 86, 28, 28, 1, 131, 131] 603 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 1457 number of broken/clashed sets: 318 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478827 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478827 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478827/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478827 Building REAL300025478828 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478828' /scratch/stefan/7787258/working/building/REAL300025478828 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478828 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478828/0 /scratch/stefan/7787258/working/building/REAL300025478828 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/722 `/scratch/stefan/7787258/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478828 none CCOC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 25, 34, 34, 36, 36, 75, 106, 201, 201, 201, 201, 201, 11, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 34, 34, 34, 75, 75, 201, 11, 11, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 35, 52, 26, 51] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 546 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478828 none CCOC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 145, 129, 145, 129, 129, 129, 111, 66, 45, 66, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 111, 111, 66, 66, 66, 27, 27, 1, 129, 129, 201, 201] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 785 number of broken/clashed sets: 133 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478828 none CCOC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 24, 38, 129, 129, 129, 129, 129, 1, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 24, 24, 129, 1, 1, 11, 11] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 25, 49, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 289 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478828 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478828 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478828/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478828 Building REAL300025478829 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478829' /scratch/stefan/7787258/working/building/REAL300025478829 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478829 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478829/0 /scratch/stefan/7787258/working/building/REAL300025478829 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/723 `/scratch/stefan/7787258/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478829 none CN(CC1CCN(C(=O)CC2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 14, 14, 14, 14, 14, 1, 8, 11, 11, 13, 13, 27, 27, 27, 27, 27, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 13, 13, 27] 50 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 120 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: REAL300025478829 none CN(CC1CCN(C(=O)CC2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 26, 27, 27, 27, 27, 28, 28, 39, 50, 50, 50, 50, 50, 27, 21, 23, 12, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 26, 26, 27, 27, 27, 27, 27, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 21, 21, 1] 50 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 198 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: REAL300025478829 none CN(CC1CCN(C(=O)CC2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 14, 14, 14, 14, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 14, 28, 34, 34, 38, 38, 50, 50, 50, 50, 50, 28, 28, 28, 20, 20, 14, 14, 14, 14, 14, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 38, 38, 50] 50 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478829 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478829 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478829/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478829 Building REAL300025478830 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478830' /scratch/stefan/7787258/working/building/REAL300025478830 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478830 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478830/0 /scratch/stefan/7787258/working/building/REAL300025478830 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/724 `/scratch/stefan/7787258/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN(C)N=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478830 none CN(CC1CCN(C(=O)C2=CN(C)N=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1, 11, 27, 27, 48, 74, 157, 157, 157, 157, 157, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 48, 48, 157] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 372 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: REAL300025478830 none CN(CC1CCN(C(=O)C2=CN(C)N=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 70, 84, 135, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 157, 38, 70, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 135, 135, 157, 157, 157, 157, 157, 201, 201, 201, 201, 157, 157, 38, 38, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 808 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: REAL300025478830 none CN(CC1CCN(C(=O)C2=CN(C)N=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 30, 60, 60, 98, 135, 201, 201, 201, 201, 201, 30, 30, 30, 18, 18, 6, 6, 6, 6, 6, 1, 2, 2, 2, 6, 6, 98, 98, 201] 201 rigid atoms, others: [36, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 572 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478830 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478830 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478830/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478830 Building REAL300025478831 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478831' /scratch/stefan/7787258/working/building/REAL300025478831 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478831 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478831/0 /scratch/stefan/7787258/working/building/REAL300025478831 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/725 `/scratch/stefan/7787258/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478831 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 22, 21, 31, 31, 31, 31, 45, 52, 52, 53, 53, 83, 120, 201, 201, 201, 201, 201, 31, 1, 2, 2, 2, 8, 8, 31, 31, 31, 31, 31, 45, 45, 52, 52, 52, 83, 83, 201, 31, 31] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 555 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: REAL300025478831 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 164, 107, 93, 107, 93, 93, 93, 84, 65, 49, 65, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 164, 164, 93, 93, 93, 93, 93, 84, 84, 65, 65, 65, 27, 27, 1, 93, 93] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 767 number of broken/clashed sets: 98 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478831 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 23, 36, 93, 93, 93, 93, 93, 1, 31, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 93, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 262 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478831 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478831 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478831/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478831 Building REAL300025478832 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478832' /scratch/stefan/7787258/working/building/REAL300025478832 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478832 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478832/0 /scratch/stefan/7787258/working/building/REAL300025478832 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/726 `/scratch/stefan/7787258/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478832 none CN(CC1CCN(C(=O)C2=NN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 11, 12, 1, 11, 25, 25, 40, 63, 120, 120, 120, 120, 120, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 40, 40, 120] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 307 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: REAL300025478832 none CN(CC1CCN(C(=O)C2=NN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 68, 74, 113, 120, 120, 120, 120, 155, 155, 201, 201, 201, 201, 201, 120, 36, 68, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 113, 113, 120, 120, 120, 120, 120, 201, 201, 201, 201, 120, 120, 36, 36, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 706 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: REAL300025478832 none CN(CC1CCN(C(=O)C2=NN(C)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 25, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 35, 68, 68, 96, 136, 201, 201, 201, 201, 201, 35, 35, 35, 25, 25, 12, 12, 12, 12, 12, 2, 2, 2, 1, 12, 12, 96, 96, 201] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 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, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478832 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478832 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478832/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478832 Building REAL300025478833 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478833' /scratch/stefan/7787258/working/building/REAL300025478833 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478833 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478833/0 /scratch/stefan/7787258/working/building/REAL300025478833 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/727 `/scratch/stefan/7787258/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478833 none CNC(=O)NCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 16, 18, 11, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 26, 41, 112, 112, 112, 112, 112, 1, 18, 18, 18, 18, 16, 11, 11, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 26, 26, 112, 1, 1] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 49, 50, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 308 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478833 none CNC(=O)NCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 156, 151, 126, 112, 126, 112, 112, 112, 90, 67, 52, 67, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 195, 156, 156, 151, 151, 112, 112, 112, 112, 112, 90, 90, 67, 67, 67, 29, 29, 1, 112, 112] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 802 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478833 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478833 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478833/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478833 Building REAL300025478834 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478834' /scratch/stefan/7787258/working/building/REAL300025478834 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478834 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478834/0 /scratch/stefan/7787258/working/building/REAL300025478834 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/728 `/scratch/stefan/7787258/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=C(F)C=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478834 none CN(CC1CCN(C(=O)C2=C(F)C=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 1, 9, 22, 22, 44, 60, 108, 108, 108, 108, 108, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 12, 12, 1, 1, 44, 44, 108] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 15, 35, 38, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 40, 41, 42]) total number of confs: 297 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478834 none CN(CC1CCN(C(=O)C2=C(F)C=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 59, 90, 108, 108, 108, 108, 115, 115, 201, 201, 201, 201, 201, 108, 33, 55, 13, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 90, 90, 108, 108, 108, 108, 108, 201, 201, 108, 108, 33, 33, 1] 201 rigid atoms, others: [42, 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: 636 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478834 none CN(CC1CCN(C(=O)C2=C(F)C=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 27, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 41, 72, 72, 112, 140, 201, 201, 201, 201, 201, 41, 41, 41, 27, 27, 12, 12, 12, 12, 12, 1, 1, 12, 12, 112, 112, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 631 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478834 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478834 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478834/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478834 Building REAL300025478835 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478835' /scratch/stefan/7787258/working/building/REAL300025478835 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478835 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478835/0 /scratch/stefan/7787258/working/building/REAL300025478835 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/729 `/scratch/stefan/7787258/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025478835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478835 none CCN1N=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 13, 17, 17, 21, 21, 44, 65, 156, 156, 156, 156, 156, 6, 1, 6, 6, 6, 5, 5, 1, 6, 6, 6, 6, 6, 13, 13, 17, 17, 17, 44, 44, 156, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 376 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478835 none CCN1N=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 156, 156, 156, 155, 135, 155, 135, 135, 135, 125, 78, 55, 78, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 135, 156, 201, 201, 201, 201, 201, 156, 135, 135, 135, 135, 135, 125, 125, 78, 78, 78, 30, 30, 1, 135, 135] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 889 number of broken/clashed sets: 103 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478835 none CCN1N=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 27, 44, 135, 135, 135, 135, 135, 1, 6, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 27, 27, 135, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478835 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478835 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478835/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478835 Building REAL300025478836 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478836' /scratch/stefan/7787258/working/building/REAL300025478836 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478836 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478836/0 /scratch/stefan/7787258/working/building/REAL300025478836 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/730 `/scratch/stefan/7787258/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(C)(C)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478836 none CN(CC1CCN(C(=O)CC(C)(C)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 50, 50, 1, 8, 11, 11, 15, 15, 42, 42, 42, 42, 42, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 1, 1, 15, 15, 42] 187 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 268 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478836 none CN(CC1CCN(C(=O)CC(C)(C)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 33, 36, 42, 42, 42, 42, 49, 49, 78, 149, 149, 149, 187, 187, 42, 30, 33, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 36, 36, 42, 42, 42, 42, 42, 78, 78, 149, 149, 149, 149, 149, 149, 187, 187, 187, 187, 187, 42, 42, 30, 30, 1] 187 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 839 number of broken/clashed sets: 122 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478836 none CN(CC1CCN(C(=O)CC(C)(C)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [108, 79, 50, 50, 50, 50, 33, 28, 33, 9, 1, 9, 9, 1, 1, 1, 50, 108, 137, 137, 153, 153, 187, 187, 187, 187, 187, 108, 108, 108, 79, 79, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 50, 50, 153, 153, 187] 187 rigid atoms, others: [47, 10, 45, 46, 13, 48, 49, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52, 53, 54]) total number of confs: 691 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478836 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478836 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478836/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478836 Building REAL300025478837 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478837' /scratch/stefan/7787258/working/building/REAL300025478837 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478837 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478837/0 /scratch/stefan/7787258/working/building/REAL300025478837 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/731 `/scratch/stefan/7787258/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478837 none CCN1N=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 11, 16, 16, 20, 20, 42, 62, 111, 111, 111, 111, 111, 4, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 11, 11, 16, 16, 16, 42, 42, 111, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 318 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478837 none CCN1N=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 111, 111, 111, 111, 111, 91, 61, 91, 61, 61, 61, 57, 44, 34, 44, 21, 34, 12, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 111, 61, 61, 61, 61, 61, 57, 57, 44, 44, 44, 21, 21, 1, 61, 61] 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, 46, 47]) total number of confs: 926 number of broken/clashed sets: 96 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478837 none CCN1N=NC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 21, 31, 61, 61, 61, 61, 61, 1, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 21, 21, 61, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478837 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478837 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478837/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478837 Building REAL300025478838 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478838' /scratch/stefan/7787258/working/building/REAL300025478838 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478838 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478838/0 /scratch/stefan/7787258/working/building/REAL300025478838 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/732 `/scratch/stefan/7787258/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478838 none CC1=CSC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 31, 45, 45, 52, 52, 76, 122, 201, 201, 201, 201, 201, 13, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 31, 31, 45, 45, 45, 76, 76, 201, 13, 13, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 550 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478838 none CC1=CSC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 144, 121, 144, 121, 121, 121, 102, 75, 51, 75, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 102, 102, 75, 75, 75, 28, 28, 1, 121, 121, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 641 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478838 none CC1=CSC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 6, 11, 11, 18, 18, 36, 56, 121, 121, 121, 121, 121, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 36, 36, 121, 1, 1, 13] 201 rigid atoms, others: [32, 33, 34, 43, 5, 7, 8, 9, 10, 11, 44, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 303 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478838 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478838 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478838/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478838 Building REAL300025478839 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478839' /scratch/stefan/7787258/working/building/REAL300025478839 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478839 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478839/0 /scratch/stefan/7787258/working/building/REAL300025478839 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/733 `/scratch/stefan/7787258/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478839 none CN(CC1CCN(C(=O)C2CC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 1, 14, 34, 34, 69, 95, 158, 158, 158, 158, 158, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 69, 69, 158] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 39, 34, 14, 38, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42]) total number of confs: 444 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478839 none CN(CC1CCN(C(=O)C2CC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 79, 92, 137, 158, 158, 158, 158, 181, 181, 201, 201, 201, 201, 158, 34, 79, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 137, 137, 158, 158, 158, 158, 158, 201, 201, 201, 158, 158, 34, 34, 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: 785 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: REAL300025478839 none CN(CC1CCN(C(=O)C2CC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 22, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 10, 36, 61, 61, 109, 140, 201, 201, 201, 201, 201, 36, 36, 36, 22, 22, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 109, 109, 201] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 607 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478839 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478839 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478839/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478839 Building REAL300025478840 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478840' /scratch/stefan/7787258/working/building/REAL300025478840 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478840 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478840/0 /scratch/stefan/7787258/working/building/REAL300025478840 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/734 `/scratch/stefan/7787258/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478840 none CCC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 10, 10, 18, 28, 84, 84, 84, 84, 84, 1, 13, 13, 13, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 18, 18, 84, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 222 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478840 none CCC(C)=CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 93, 84, 93, 84, 84, 84, 71, 58, 44, 58, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 123, 123, 123, 123, 84, 84, 84, 84, 84, 71, 71, 58, 58, 58, 28, 28, 1, 84, 84] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 944 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478840 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478840 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478840/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478840 Building REAL300025478841 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478841' /scratch/stefan/7787258/working/building/REAL300025478841 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478841 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478841/0 /scratch/stefan/7787258/working/building/REAL300025478841 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/735 `/scratch/stefan/7787258/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478841 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 23, 37, 37, 54, 54, 83, 126, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 37, 37, 37, 83, 83, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 568 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478841 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 135, 116, 135, 116, 116, 116, 99, 78, 58, 78, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 99, 99, 78, 78, 78, 29, 29, 1, 116, 116] 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, 46, 47]) total number of confs: 638 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478841 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 5, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 34, 53, 116, 116, 116, 116, 116, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 34, 34, 116, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478841 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478841 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478841/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478841 Building REAL300025478842 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478842' /scratch/stefan/7787258/working/building/REAL300025478842 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478842 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478842/0 /scratch/stefan/7787258/working/building/REAL300025478842 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/736 `/scratch/stefan/7787258/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478842 none CC(C)C#CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 14, 14, 34, 34, 61, 100, 179, 179, 179, 179, 179, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 61, 61, 179, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 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: REAL300025478842 none CC(C)C#CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 179, 201, 179, 179, 179, 151, 95, 51, 95, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 151, 151, 95, 95, 95, 27, 27, 1, 179, 179] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 768 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478842 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478842 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478842/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478842 Building REAL300025478843 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478843' /scratch/stefan/7787258/working/building/REAL300025478843 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478843 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478843/0 /scratch/stefan/7787258/working/building/REAL300025478843 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/737 `/scratch/stefan/7787258/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1) `REAL300025478843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478843 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 26, 40, 40, 56, 56, 83, 122, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 26, 26, 40, 40, 40, 83, 83, 201, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 45, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 580 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478843 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 119, 140, 119, 119, 119, 99, 71, 54, 71, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 99, 99, 71, 71, 71, 29, 29, 1, 119, 119, 201, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 658 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478843 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 36, 55, 119, 119, 119, 119, 119, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 36, 36, 119, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 289 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478843 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478843 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478843/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478843 Building REAL300025478844 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478844' /scratch/stefan/7787258/working/building/REAL300025478844 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478844 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478844/0 /scratch/stefan/7787258/working/building/REAL300025478844 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/738 `/scratch/stefan/7787258/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2(O)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478844 none CN(CC1CCN(C(=O)CC2(O)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 13, 17, 17, 17, 17, 1, 8, 11, 11, 15, 15, 34, 34, 34, 34, 34, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 13, 13, 51, 17, 17, 17, 17, 17, 17, 1, 1, 15, 15, 34] 162 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478844 none CN(CC1CCN(C(=O)CC2(O)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 31, 34, 34, 34, 34, 38, 38, 52, 54, 54, 54, 54, 34, 26, 29, 13, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 31, 31, 34, 34, 34, 34, 34, 52, 52, 162, 54, 54, 54, 54, 54, 54, 34, 34, 26, 26, 1] 162 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 374 number of broken/clashed sets: 87 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478844 none CN(CC1CCN(C(=O)CC2(O)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [30, 24, 17, 17, 17, 17, 11, 5, 11, 1, 1, 1, 1, 1, 1, 17, 30, 38, 38, 44, 44, 54, 54, 54, 54, 54, 30, 30, 30, 24, 24, 17, 17, 17, 17, 17, 5, 5, 6, 1, 1, 1, 1, 1, 1, 17, 17, 44, 44, 54] 162 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 42] 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, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478844 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478844 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478844/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478844 Building REAL300025478845 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478845' /scratch/stefan/7787258/working/building/REAL300025478845 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478845 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478845/0 /scratch/stefan/7787258/working/building/REAL300025478845 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/739 `/scratch/stefan/7787258/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478845 none CC1=CNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 23, 34, 34, 53, 53, 79, 127, 201, 201, 201, 201, 201, 7, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 23, 23, 34, 34, 34, 79, 79, 201, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 550 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478845 none CC1=CNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 189, 158, 189, 158, 158, 158, 143, 101, 63, 101, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 158, 158, 158, 158, 158, 143, 143, 101, 101, 101, 30, 30, 1, 158, 158] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 750 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478845 none CC1=CNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 13, 13, 26, 26, 45, 74, 158, 158, 158, 158, 158, 1, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 45, 45, 158, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 369 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478845 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478845 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478845/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478845 Building REAL300025478846 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478846' /scratch/stefan/7787258/working/building/REAL300025478846 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478846 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478846/0 /scratch/stefan/7787258/working/building/REAL300025478846 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/740 `/scratch/stefan/7787258/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1) `REAL300025478846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478846 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 4, 1, 1, 1, 1, 1, 6, 11, 11, 20, 20, 36, 55, 119, 119, 119, 119, 119, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 36, 36, 119, 1, 1, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 42, 43, 21, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 298 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478846 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 8, 8, 8, 8, 24, 34, 34, 52, 52, 77, 116, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 24, 24, 34, 34, 34, 77, 77, 201, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 535 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478846 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 119, 131, 119, 119, 119, 96, 76, 55, 76, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 96, 96, 76, 76, 76, 27, 27, 1, 119, 119, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 772 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478846 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478846 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478846/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478846 Building REAL300025478847 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478847' /scratch/stefan/7787258/working/building/REAL300025478847 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478847 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478847/0 /scratch/stefan/7787258/working/building/REAL300025478847 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/741 `/scratch/stefan/7787258/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C#CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478847 none CN(CC1CCN(C(=O)C#CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 1, 13, 33, 33, 78, 102, 160, 160, 160, 160, 160, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 2, 1, 1, 78, 78, 160] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478847 none CN(CC1CCN(C(=O)C#CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 61, 90, 134, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 160, 31, 61, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 134, 134, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 160, 160, 31, 31, 1] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 819 number of broken/clashed sets: 102 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478847 none CN(CC1CCN(C(=O)C#CC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 48, 48, 107, 140, 201, 201, 201, 201, 201, 22, 22, 22, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 107, 107, 201] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 39, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478847 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478847 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478847/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478847 Building REAL300025478848 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478848' /scratch/stefan/7787258/working/building/REAL300025478848 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478848 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478848/0 /scratch/stefan/7787258/working/building/REAL300025478848 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/742 `/scratch/stefan/7787258/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C#CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478848 none CN(CC1CCN(C(=O)C#CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 13, 32, 32, 80, 104, 164, 164, 164, 164, 164, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 80, 80, 164] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 470 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478848 none CN(CC1CCN(C(=O)C#CC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 95, 139, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 164, 35, 64, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 139, 139, 164, 164, 164, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 35, 35, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 823 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478848 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478848 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478848/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478848 Building REAL300025478849 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478849' /scratch/stefan/7787258/working/building/REAL300025478849 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478849 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478849/0 /scratch/stefan/7787258/working/building/REAL300025478849 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/743 `/scratch/stefan/7787258/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1) `REAL300025478849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478849 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 12, 12, 17, 17, 17, 17, 33, 42, 42, 47, 47, 79, 113, 201, 201, 201, 201, 201, 17, 1, 2, 2, 2, 6, 6, 17, 17, 17, 17, 17, 33, 33, 42, 42, 42, 79, 79, 201, 17, 17, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 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: REAL300025478849 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 110, 87, 110, 87, 87, 87, 78, 56, 42, 56, 26, 42, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 78, 78, 56, 56, 56, 26, 26, 1, 87, 87, 201] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 827 number of broken/clashed sets: 95 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478849 none CC1=NN=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 25, 40, 87, 87, 87, 87, 87, 1, 17, 17, 17, 17, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 25, 25, 87, 1, 1, 17] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 251 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478849 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478849 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478849/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478849 Building REAL300025478850 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478850' /scratch/stefan/7787258/working/building/REAL300025478850 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478850 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478850/0 /scratch/stefan/7787258/working/building/REAL300025478850 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/744 `/scratch/stefan/7787258/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1) `REAL300025478850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478850 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 7, 20, 27, 27, 45, 45, 81, 122, 201, 201, 201, 201, 201, 6, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 20, 20, 27, 27, 27, 81, 81, 201, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 565 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478850 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 201, 142, 142, 142, 128, 87, 64, 87, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 142, 128, 128, 87, 87, 87, 29, 29, 1, 142, 142] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 747 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478850 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 22, 22, 45, 69, 142, 142, 142, 142, 142, 1, 6, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 45, 45, 142, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478850 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478850 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478850/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478850 Building REAL300025478851 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478851' /scratch/stefan/7787258/working/building/REAL300025478851 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478851 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478851/0 /scratch/stefan/7787258/working/building/REAL300025478851 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/745 `/scratch/stefan/7787258/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478851 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 15, 15, 1, 6, 6, 6, 8, 8, 16, 16, 16, 16, 16, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 12, 12, 1, 1, 8, 8, 16] 30 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478851 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 30, 30, 30, 30, 30, 30, 30, 16, 15, 16, 11, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 30, 30, 16, 16, 15, 15, 1] 30 rigid atoms, others: [44, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478851 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 12, 19, 19, 19, 23, 23, 30, 30, 30, 30, 30, 19, 19, 19, 16, 16, 12, 12, 12, 12, 12, 1, 1, 12, 12, 23, 23, 30] 30 rigid atoms, others: [38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478851 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478851 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478851/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478851 Building REAL300025478852 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478852' /scratch/stefan/7787258/working/building/REAL300025478852 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478852 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478852/0 /scratch/stefan/7787258/working/building/REAL300025478852 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/746 `/scratch/stefan/7787258/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)N=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478852 none CC1=CN(C)N=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 24, 36, 36, 53, 53, 79, 122, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 24, 24, 36, 36, 36, 79, 79, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 551 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478852 none CC1=CN(C)N=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 187, 155, 187, 155, 155, 155, 138, 94, 62, 94, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 155, 138, 138, 94, 94, 94, 28, 28, 1, 155, 155] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 729 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478852 none CC1=CN(C)N=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 6, 13, 13, 27, 27, 48, 76, 155, 155, 155, 155, 155, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 48, 48, 155, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 373 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478852 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478852 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478852/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478852 Building REAL300025478853 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478853' /scratch/stefan/7787258/working/building/REAL300025478853 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478853 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478853/0 /scratch/stefan/7787258/working/building/REAL300025478853 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/747 `/scratch/stefan/7787258/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478853 none CN(CC1CCN(C(=O)C2CCCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 1, 14, 33, 33, 62, 85, 140, 140, 140, 140, 140, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 62, 62, 140] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 381 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478853 none CN(CC1CCN(C(=O)C2CCCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 77, 93, 122, 140, 140, 140, 140, 146, 146, 201, 201, 201, 201, 201, 201, 140, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 122, 122, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 38, 38, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 804 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478853 none CN(CC1CCN(C(=O)C2CCCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 32, 65, 65, 103, 140, 201, 201, 201, 201, 201, 32, 32, 32, 18, 18, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 103, 103, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51]) total number of confs: 574 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478853 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478853 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478853/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478853 Building REAL300025478854 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478854' /scratch/stefan/7787258/working/building/REAL300025478854 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478854 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478854/0 /scratch/stefan/7787258/working/building/REAL300025478854 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/748 `/scratch/stefan/7787258/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478854 none CN(CC1CCN(C(=O)CC2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 21, 41, 41, 41, 41, 41, 1, 9, 14, 14, 23, 24, 53, 53, 53, 53, 53, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 21, 21, 41, 41, 41, 41, 41, 1, 1, 23, 23, 53] 160 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478854 none CN(CC1CCN(C(=O)CC2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [42, 40, 42, 47, 53, 53, 53, 53, 82, 82, 151, 160, 160, 160, 160, 160, 53, 32, 40, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 47, 47, 53, 53, 53, 53, 53, 151, 151, 160, 160, 160, 160, 160, 53, 53, 32, 32, 1] 160 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 639 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478854 none CN(CC1CCN(C(=O)CC2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [83, 63, 41, 41, 41, 41, 25, 9, 25, 1, 1, 1, 1, 1, 1, 1, 41, 83, 103, 103, 124, 124, 160, 160, 160, 160, 160, 83, 83, 83, 63, 63, 41, 41, 41, 41, 41, 9, 9, 2, 2, 2, 1, 1, 41, 41, 124, 124, 160] 160 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 526 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478854 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478854 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478854/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478854 Building REAL300025478855 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478855' /scratch/stefan/7787258/working/building/REAL300025478855 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478855 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478855/0 /scratch/stefan/7787258/working/building/REAL300025478855 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/749 `/scratch/stefan/7787258/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478855 none COCC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 7, 17, 17, 32, 32, 32, 32, 66, 77, 77, 93, 93, 100, 135, 189, 189, 189, 189, 189, 32, 1, 1, 11, 11, 11, 7, 7, 7, 7, 32, 32, 32, 32, 32, 66, 66, 77, 77, 77, 100, 100, 189, 32, 32, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 49, 50, 51, 52, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 602 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: REAL300025478855 none COCC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 147, 52, 45, 52, 45, 45, 45, 39, 30, 25, 30, 17, 25, 12, 1, 1, 1, 1, 1, 1, 1, 45, 189, 189, 201, 201, 201, 201, 201, 147, 147, 45, 45, 45, 45, 45, 39, 39, 30, 30, 30, 17, 17, 1, 45, 45, 189, 189, 189, 189] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 806 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: REAL300025478855 none COCC1(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 48, 32, 15, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 19, 24, 45, 45, 45, 45, 45, 1, 32, 32, 56, 56, 56, 48, 48, 15, 15, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 19, 19, 45, 1, 1, 32, 32, 32, 32] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 312 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478855 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478855 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478855/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478855 Building REAL300025478856 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478856' /scratch/stefan/7787258/working/building/REAL300025478856 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478856 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478856/0 /scratch/stefan/7787258/working/building/REAL300025478856 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/750 `/scratch/stefan/7787258/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478856 none CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 12, 12, 31, 31, 56, 87, 176, 176, 176, 176, 176, 1, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 56, 56, 176, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 41, 40, 21, 27, 28, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 447 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478856 none CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 176, 188, 176, 176, 176, 164, 103, 86, 103, 40, 86, 13, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 201, 201, 201, 176, 176, 176, 176, 176, 164, 164, 103, 103, 103, 40, 40, 1, 176, 176] 201 rigid atoms, others: [39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 842 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478856 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478856 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478856/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478856 Building REAL300025478857 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478857' /scratch/stefan/7787258/working/building/REAL300025478857 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478857 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478857/0 /scratch/stefan/7787258/working/building/REAL300025478857 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/751 `/scratch/stefan/7787258/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478857 none COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 30, 49, 131, 131, 131, 131, 131, 1, 16, 16, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 30, 30, 131, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 327 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478857 none COCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 131, 171, 131, 131, 131, 116, 72, 53, 72, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 131, 116, 116, 72, 72, 72, 30, 30, 1, 131, 131] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 848 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478857 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478857 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478857/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478857 Building REAL300025478858 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478858' /scratch/stefan/7787258/working/building/REAL300025478858 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478858 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478858/0 /scratch/stefan/7787258/working/building/REAL300025478858 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/752 `/scratch/stefan/7787258/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478858 none CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 13, 13, 34, 34, 81, 104, 170, 170, 170, 170, 170, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 81, 81, 170, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478858 none CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 201, 170, 170, 170, 156, 110, 78, 110, 38, 78, 13, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 170, 170, 170, 170, 170, 156, 156, 110, 110, 110, 38, 38, 1, 170, 170] 201 rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 813 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478858 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478858 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478858/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478858 Building REAL300025478859 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478859' /scratch/stefan/7787258/working/building/REAL300025478859 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478859 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478859/0 /scratch/stefan/7787258/working/building/REAL300025478859 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/753 `/scratch/stefan/7787258/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478859 none CN(CC1CCN(C(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 1, 10, 23, 23, 43, 59, 119, 119, 119, 119, 119, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 43, 43, 119] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 39, 12, 38, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 326 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478859 none CN(CC1CCN(C(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 69, 75, 111, 119, 119, 119, 119, 122, 122, 201, 201, 119, 37, 69, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 111, 111, 119, 119, 119, 119, 119, 201, 201, 201, 201, 201, 119, 119, 37, 37, 1] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 810 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478859 none CN(CC1CCN(C(=O)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 10, 30, 58, 58, 100, 129, 201, 201, 201, 201, 201, 30, 30, 30, 22, 22, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 100, 100, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 595 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478859 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478859 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478859/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478859 Building REAL300025478860 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478860' /scratch/stefan/7787258/working/building/REAL300025478860 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478860 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478860/0 /scratch/stefan/7787258/working/building/REAL300025478860 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/754 `/scratch/stefan/7787258/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478860 none CN(CC1CCN(C(=O)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 1, 11, 27, 27, 48, 64, 120, 120, 120, 120, 120, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 48, 48, 120] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 326 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478860 none CN(CC1CCN(C(=O)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 71, 79, 112, 120, 120, 120, 120, 125, 125, 201, 201, 201, 120, 37, 71, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 112, 112, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 120, 120, 37, 37, 1] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 799 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478860 none CN(CC1CCN(C(=O)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 8, 29, 61, 61, 95, 125, 201, 201, 201, 201, 201, 29, 29, 29, 19, 19, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 95, 95, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45]) total number of confs: 580 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478860 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478860 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478860/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478860 Building REAL300025478861 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478861' /scratch/stefan/7787258/working/building/REAL300025478861 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478861 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478861/0 /scratch/stefan/7787258/working/building/REAL300025478861 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/755 `/scratch/stefan/7787258/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478861 none CN(CC1CCN(C(=O)C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 1, 13, 31, 31, 57, 74, 133, 133, 133, 133, 133, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 57, 57, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 371 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478861 none CN(CC1CCN(C(=O)C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 71, 83, 119, 133, 133, 133, 133, 138, 138, 201, 201, 201, 201, 133, 36, 71, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 119, 119, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 36, 36, 1] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 809 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478861 none CN(CC1CCN(C(=O)C2CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 9, 33, 63, 63, 103, 130, 201, 201, 201, 201, 201, 33, 33, 33, 20, 20, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 103, 103, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 586 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478861 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478861 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478861/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478861 Building REAL300025478862 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478862' /scratch/stefan/7787258/working/building/REAL300025478862 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478862 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478862/0 /scratch/stefan/7787258/working/building/REAL300025478862 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/756 `/scratch/stefan/7787258/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478862 none CN(CC1CCN(C(=O)C2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 13, 31, 31, 60, 83, 133, 133, 133, 133, 133, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 60, 60, 133] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 368 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478862 none CN(CC1CCN(C(=O)C2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 71, 87, 118, 133, 133, 133, 133, 136, 136, 201, 201, 201, 201, 201, 133, 38, 71, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 118, 118, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 38, 38, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 801 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478862 none CN(CC1CCN(C(=O)C2CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 30, 61, 61, 103, 141, 201, 201, 201, 201, 201, 30, 30, 30, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 103, 103, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 581 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478862 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478862 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478862/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478862 Building REAL300025478863 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478863' /scratch/stefan/7787258/working/building/REAL300025478863 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478863 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478863/0 /scratch/stefan/7787258/working/building/REAL300025478863 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/757 `/scratch/stefan/7787258/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478863 none CN(CC1CCN(C(=O)CC2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 14, 22, 22, 22, 22, 22, 1, 8, 12, 12, 18, 19, 39, 39, 39, 39, 39, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 14, 14, 22, 22, 22, 22, 22, 22, 1, 1, 18, 18, 39] 78 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478863 none CN(CC1CCN(C(=O)CC2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 29, 31, 34, 39, 39, 39, 39, 43, 43, 72, 78, 78, 78, 78, 78, 39, 24, 29, 13, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 34, 34, 39, 39, 39, 39, 39, 72, 72, 78, 78, 78, 78, 78, 78, 39, 39, 24, 24, 1] 78 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 307 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478863 none CN(CC1CCN(C(=O)CC2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 22, 22, 22, 22, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 22, 50, 58, 58, 63, 63, 78, 78, 78, 78, 78, 50, 50, 50, 37, 37, 22, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 22, 22, 63, 63, 78] 78 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 266 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478863 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478863 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478863/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478863 Building REAL300025478864 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478864' /scratch/stefan/7787258/working/building/REAL300025478864 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478864 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478864/0 /scratch/stefan/7787258/working/building/REAL300025478864 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/758 `/scratch/stefan/7787258/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478864 none CNC(=O)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 3, 3, 6, 6, 6, 6, 15, 25, 25, 44, 44, 67, 107, 201, 201, 201, 201, 201, 6, 1, 1, 4, 4, 4, 4, 6, 6, 6, 6, 6, 15, 15, 25, 25, 25, 67, 67, 201, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [2, 4, 5, 46, 47, 48, 49, 25, 26] set([0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 508 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: REAL300025478864 none CNC(=O)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 187, 165, 187, 165, 165, 165, 144, 90, 49, 90, 25, 49, 13, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 144, 144, 90, 90, 90, 25, 25, 1, 165, 165, 201, 201, 201, 201] 201 rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 767 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: REAL300025478864 none CNC(=O)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 4, 1, 4, 1, 1, 1, 1, 1, 5, 13, 13, 30, 30, 52, 85, 165, 165, 165, 165, 165, 1, 6, 6, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 52, 52, 165, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 44, 45, 24, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 421 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478864 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478864 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478864/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478864 Building REAL300025478865 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478865' /scratch/stefan/7787258/working/building/REAL300025478865 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478865 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478865/0 /scratch/stefan/7787258/working/building/REAL300025478865 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/759 `/scratch/stefan/7787258/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478865 none CN(CC1CCN(C(=O)C2=NN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1, 12, 28, 28, 50, 80, 153, 153, 153, 153, 153, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 50, 50, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 373 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478865 none CN(CC1CCN(C(=O)C2=NN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 77, 89, 136, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 153, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 136, 136, 153, 153, 153, 153, 153, 201, 201, 201, 201, 153, 153, 39, 39, 1] 201 rigid atoms, others: [44, 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]) total number of confs: 803 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478865 none CN(CC1CCN(C(=O)C2=NN(C)N=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 26, 52, 52, 90, 134, 201, 201, 201, 201, 201, 26, 26, 26, 15, 15, 6, 6, 6, 6, 6, 2, 2, 2, 1, 6, 6, 90, 90, 201] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 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, 40, 41, 42, 43, 44]) total number of confs: 554 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478865 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478865 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478865/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478865 Building REAL300025478866 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478866' /scratch/stefan/7787258/working/building/REAL300025478866 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478866 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478866/0 /scratch/stefan/7787258/working/building/REAL300025478866 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/760 `/scratch/stefan/7787258/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1) `REAL300025478866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478866 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 29, 41, 41, 50, 50, 79, 116, 201, 201, 201, 201, 201, 11, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 29, 29, 41, 41, 41, 79, 79, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 563 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478866 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 118, 131, 118, 118, 118, 104, 73, 48, 73, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 118, 104, 104, 73, 73, 73, 26, 26, 1, 118, 118, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 621 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478866 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 38, 56, 118, 118, 118, 118, 118, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 38, 38, 118, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 306 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478866 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478866 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478866/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478866 Building REAL300025478867 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478867' /scratch/stefan/7787258/working/building/REAL300025478867 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478867 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478867/0 /scratch/stefan/7787258/working/building/REAL300025478867 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/761 `/scratch/stefan/7787258/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478867 none CN(CC1CCN(C(=O)C2(C)CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 13, 28, 28, 56, 75, 128, 128, 128, 128, 128, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 56, 56, 128] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 359 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478867 none CN(CC1CCN(C(=O)C2(C)CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 72, 89, 116, 128, 128, 128, 128, 166, 166, 201, 201, 201, 201, 201, 201, 128, 35, 72, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 116, 116, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 35, 35, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 804 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478867 none CN(CC1CCN(C(=O)C2(C)CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 34, 66, 66, 111, 145, 201, 201, 201, 201, 201, 34, 34, 34, 16, 16, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 111, 111, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52]) total number of confs: 614 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478867 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478867 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478867/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478867 Building REAL300025478868 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478868' /scratch/stefan/7787258/working/building/REAL300025478868 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478868 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478868/0 /scratch/stefan/7787258/working/building/REAL300025478868 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/762 `/scratch/stefan/7787258/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478868 none CC(C)CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 20, 14, 20, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 21, 32, 89, 89, 89, 89, 89, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 20, 20, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 21, 21, 89, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 278 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478868 none CC(C)CC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 188, 201, 89, 89, 89, 89, 89, 89, 75, 48, 36, 48, 26, 36, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 89, 89, 89, 89, 89, 75, 75, 48, 48, 48, 26, 26, 1, 89, 89] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 849 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478868 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478868 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478868/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478868 Building REAL300025478869 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478869' /scratch/stefan/7787258/working/building/REAL300025478869 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478869 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478869/0 /scratch/stefan/7787258/working/building/REAL300025478869 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/763 `/scratch/stefan/7787258/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478869 none CC1=NN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 27, 38, 38, 54, 54, 82, 124, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 27, 27, 38, 38, 38, 82, 82, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 566 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: REAL300025478869 none CC1=NN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 153, 132, 153, 132, 132, 132, 115, 74, 58, 74, 28, 58, 12, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 115, 115, 74, 74, 74, 28, 28, 1, 132, 132] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 688 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: REAL300025478869 none CC1=NN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 38, 59, 132, 132, 132, 132, 132, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 38, 38, 132, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 9, 10, 11, 12, 13, 46, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 312 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478869 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478869 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478869/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478869 Building REAL300025478870 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478870' /scratch/stefan/7787258/working/building/REAL300025478870 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478870 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478870/0 /scratch/stefan/7787258/working/building/REAL300025478870 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/764 `/scratch/stefan/7787258/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CC[N@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 2, 1, 1, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5] 6 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 37 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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 1] 6 rigid atoms, others: [54, 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, 19, 20, 28, 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: 17 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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 6, 6, 6] 6 rigid atoms, others: [48, 43, 40, 9, 10, 11, 12, 13, 14, 44, 16, 49, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 27 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478870 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478870/1 /scratch/stefan/7787258/working/building/REAL300025478870 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/765 `/scratch/stefan/7787258/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CC[N@@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478870.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 9, 12, 12, 12, 12, 12, 12, 1, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 11] 18 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 72 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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 17, 18, 18, 18, 18, 18, 18, 11, 9, 11, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 9, 9, 1] 18 rigid atoms, others: [54, 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, 19, 20, 28, 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: 60 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: REAL300025478870 none CN(CC1CCN(C(=O)CC2CC[N@@H+](C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 17, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 12, 17, 17, 18] 18 rigid atoms, others: [48, 43, 40, 9, 10, 11, 12, 13, 14, 44, 16, 49, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478870 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478870 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478870/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478870/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478870 Building REAL300025478871 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478871' /scratch/stefan/7787258/working/building/REAL300025478871 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478871 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478871/0 /scratch/stefan/7787258/working/building/REAL300025478871 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/766 `/scratch/stefan/7787258/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478871 none CN(CC1CCN(C(=O)CC2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 31, 31, 31, 31, 31, 1, 9, 14, 14, 22, 23, 53, 53, 53, 53, 53, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 31, 31, 31, 31, 31, 1, 1, 22, 22, 53] 108 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478871 none CN(CC1CCN(C(=O)CC2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [42, 40, 42, 47, 53, 53, 53, 53, 66, 66, 98, 108, 108, 108, 108, 108, 53, 31, 40, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 47, 47, 53, 53, 53, 53, 53, 98, 98, 108, 108, 108, 108, 108, 53, 53, 31, 31, 1] 108 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 416 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478871 none CN(CC1CCN(C(=O)CC2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [56, 44, 31, 31, 31, 31, 19, 6, 19, 1, 1, 1, 1, 1, 1, 1, 31, 56, 67, 67, 83, 83, 108, 108, 108, 108, 108, 56, 56, 56, 44, 44, 31, 31, 31, 31, 31, 6, 6, 1, 1, 2, 2, 2, 31, 31, 83, 83, 108] 108 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 365 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478871 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478871 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478871/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478871 Building REAL300025478872 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478872' /scratch/stefan/7787258/working/building/REAL300025478872 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478872 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478872/0 /scratch/stefan/7787258/working/building/REAL300025478872 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/767 `/scratch/stefan/7787258/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1) `REAL300025478872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478872 none CCN1C=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 14, 18, 18, 23, 23, 39, 60, 120, 120, 120, 120, 120, 6, 1, 3, 3, 3, 3, 3, 1, 5, 5, 6, 6, 6, 14, 14, 18, 18, 18, 39, 39, 120, 6, 6, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 48, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 309 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478872 none CCN1C=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 120, 120, 120, 120, 118, 105, 118, 105, 105, 105, 101, 89, 59, 89, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 105, 120, 201, 201, 201, 201, 201, 120, 105, 105, 105, 105, 105, 101, 101, 89, 89, 89, 27, 27, 1, 105, 105, 120] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 902 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478872 none CCN1C=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 12, 12, 26, 43, 105, 105, 105, 105, 105, 1, 6, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 26, 26, 105, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 273 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478872 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478872 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478872/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478872 Building REAL300025478873 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478873' /scratch/stefan/7787258/working/building/REAL300025478873 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478873 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478873/0 /scratch/stefan/7787258/working/building/REAL300025478873 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/768 `/scratch/stefan/7787258/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478873 none CCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 4, 1, 4, 1, 1, 1, 1, 1, 4, 6, 6, 10, 10, 19, 29, 74, 74, 74, 74, 74, 1, 6, 8, 8, 8, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 74, 1, 1, 8, 8, 8, 8, 8, 8] 81 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 46, 47, 35, 22, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 187 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478873 none CCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 74, 81, 74, 74, 74, 62, 59, 49, 59, 32, 49, 13, 1, 1, 1, 1, 1, 1, 1, 74, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 74, 74, 74, 74, 74, 62, 62, 59, 59, 59, 32, 32, 1, 74, 74, 81, 81, 81, 81, 81, 81] 81 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 293 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478873 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478873 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478873/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478873 Building REAL300025478874 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478874' /scratch/stefan/7787258/working/building/REAL300025478874 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478874 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478874/0 /scratch/stefan/7787258/working/building/REAL300025478874 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/769 `/scratch/stefan/7787258/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)O1) `REAL300025478874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478874 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 10, 18, 18, 44, 44, 78, 122, 201, 201, 201, 201, 201, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 18, 18, 18, 78, 78, 201, 4, 4, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 536 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: REAL300025478874 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 175, 201, 175, 175, 175, 159, 107, 57, 107, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 159, 159, 107, 107, 107, 27, 27, 1, 175, 175, 201, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 761 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: REAL300025478874 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 5, 12, 12, 31, 31, 64, 101, 175, 175, 175, 175, 175, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 64, 64, 175, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 47, 48, 23, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 451 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478874 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478874 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478874/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478874 Building REAL300025478875 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478875' /scratch/stefan/7787258/working/building/REAL300025478875 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478875 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478875/0 /scratch/stefan/7787258/working/building/REAL300025478875 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/770 `/scratch/stefan/7787258/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478875 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 12, 12, 12, 1, 7, 8, 8, 9, 9, 17, 17, 17, 17, 17, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 9, 9, 17] 22 rigid atoms, others: [51, 34, 3, 4, 5, 6, 7, 2, 50, 18, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 84 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: REAL300025478875 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 22, 22, 22, 22, 22, 22, 22, 22, 17, 14, 16, 11, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 14, 14, 1] 22 rigid atoms, others: [54, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 57 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: REAL300025478875 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 11, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 15, 15, 16, 16, 22, 22, 22, 22, 22, 14, 14, 14, 11, 11, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 16, 16, 22] 22 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 7] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478875 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478875 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478875/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478875 Building REAL300025478876 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478876' /scratch/stefan/7787258/working/building/REAL300025478876 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478876 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478876/0 /scratch/stefan/7787258/working/building/REAL300025478876 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/771 `/scratch/stefan/7787258/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025478876 none CC1CC1C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 7, 7, 7, 7, 18, 28, 28, 45, 45, 81, 121, 201, 201, 201, 201, 201, 7, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 7, 7, 18, 18, 28, 28, 28, 81, 81, 201, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 555 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478876 none CC1CC1C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 197, 178, 197, 178, 178, 178, 149, 86, 55, 86, 25, 55, 12, 1, 1, 1, 1, 1, 1, 1, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 178, 178, 178, 149, 149, 86, 86, 86, 25, 25, 1, 178, 178] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 776 number of broken/clashed sets: 57 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478876 none CC1CC1C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 6, 12, 12, 25, 25, 57, 93, 178, 178, 178, 178, 178, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 57, 57, 178, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 460 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478876 none CC1CC1C1CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 11, 18, 18, 32, 32, 65, 108, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 18, 18, 18, 65, 65, 201, 4, 4] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 3, 36, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 511 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478876 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478876 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478876/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478876 Building REAL300025478877 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478877' /scratch/stefan/7787258/working/building/REAL300025478877 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478877 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478877/0 /scratch/stefan/7787258/working/building/REAL300025478877 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/772 `/scratch/stefan/7787258/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025478877 none CN(CC1CCN(C(=O)C[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 12, 41, 41, 41, 41, 41, 70, 70, 1, 8, 12, 12, 16, 16, 37, 37, 37, 37, 37, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 13, 13, 41, 41, 70, 70, 70, 70, 70, 1, 1, 16, 16, 37] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 2, 48, 49, 18, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 316 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478877 none CN(CC1CCN(C(=O)C[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 31, 33, 33, 37, 37, 37, 37, 40, 40, 118, 196, 196, 196, 196, 196, 201, 201, 37, 26, 31, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 37, 37, 37, 37, 37, 118, 118, 196, 196, 201, 201, 201, 201, 201, 37, 37, 26, 26, 1] 201 rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 738 number of broken/clashed sets: 153 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478877 none CN(CC1CCN(C(=O)C[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 98, 70, 70, 70, 70, 53, 20, 53, 5, 5, 5, 5, 1, 5, 1, 1, 1, 70, 130, 154, 154, 168, 168, 201, 201, 201, 201, 201, 130, 130, 130, 98, 98, 70, 70, 70, 70, 70, 20, 20, 5, 5, 1, 1, 1, 1, 1, 70, 70, 168, 168, 201] 201 rigid atoms, others: [45, 43, 44, 13, 46, 15, 16, 17, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51, 52]) total number of confs: 706 number of broken/clashed sets: 153 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478877 none CN(CC1CCN(C(=O)C[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 68, 41, 41, 41, 41, 28, 7, 28, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 104, 128, 128, 142, 142, 196, 196, 196, 196, 196, 104, 104, 104, 68, 68, 41, 41, 41, 41, 41, 7, 7, 1, 1, 5, 5, 5, 5, 5, 41, 41, 142, 142, 196] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 651 number of broken/clashed sets: 153 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478877 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478877 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478877/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478877 Building REAL300025478878 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478878' /scratch/stefan/7787258/working/building/REAL300025478878 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478878 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478878/0 /scratch/stefan/7787258/working/building/REAL300025478878 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/773 `/scratch/stefan/7787258/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478878 none CC1COC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 27, 42, 42, 58, 58, 82, 123, 201, 201, 201, 201, 201, 10, 1, 2, 2, 2, 1, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 42, 42, 42, 82, 82, 201, 10, 10, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 48, 49, 25, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 551 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478878 none CC1COC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 164, 183, 164, 164, 164, 140, 90, 60, 90, 26, 60, 12, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 140, 140, 90, 90, 90, 26, 26, 1, 164, 164, 201, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 774 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478878 none CC1COC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 29, 29, 49, 77, 164, 164, 164, 164, 164, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 49, 49, 164, 1, 1, 10, 10] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 397 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478878 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478878 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478878/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478878 Building REAL300025478879 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478879' /scratch/stefan/7787258/working/building/REAL300025478879 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478879 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478879/0 /scratch/stefan/7787258/working/building/REAL300025478879 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/774 `/scratch/stefan/7787258/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@]23C[C@H]2CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478879 none CN(CC1CCN(C(=O)[C@]23C[C@H]2CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 1, 14, 34, 34, 79, 107, 178, 178, 178, 178, 178, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 79, 79, 178] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 491 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: REAL300025478879 none CN(CC1CCN(C(=O)[C@]23C[C@H]2CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 71, 104, 156, 178, 178, 178, 178, 180, 180, 201, 201, 201, 201, 201, 201, 178, 38, 71, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 156, 156, 178, 178, 178, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 38, 38, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 783 number of broken/clashed sets: 95 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478879 none CN(CC1CCN(C(=O)[C@]23C[C@H]2CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 12, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 24, 49, 49, 100, 134, 201, 201, 201, 201, 201, 24, 24, 24, 12, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 100, 100, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49]) total number of confs: 573 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478879 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478879 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478879/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478879 Building REAL300025478880 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478880' /scratch/stefan/7787258/working/building/REAL300025478880 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478880 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478880/0 /scratch/stefan/7787258/working/building/REAL300025478880 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/775 `/scratch/stefan/7787258/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478880 none CC[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 20, 29, 29, 47, 47, 74, 116, 201, 201, 201, 201, 201, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 29, 29, 29, 74, 74, 201, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 526 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478880 none CC[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 190, 201, 170, 190, 170, 170, 170, 146, 102, 69, 102, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 146, 146, 102, 102, 102, 30, 30, 1, 170, 170] 201 rigid atoms, others: [50, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 772 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478880 none CC[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 24, 24, 50, 78, 170, 170, 170, 170, 170, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 50, 50, 170, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 51, 52, 41, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 411 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478880 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478880 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478880/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478880 Building REAL300025478881 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478881' /scratch/stefan/7787258/working/building/REAL300025478881 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478881 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478881/0 /scratch/stefan/7787258/working/building/REAL300025478881 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/776 `/scratch/stefan/7787258/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1) `REAL300025478881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478881 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 11, 16, 16, 22, 22, 42, 63, 134, 134, 134, 134, 134, 4, 1, 1, 7, 7, 7, 6, 6, 1, 5, 5, 5, 5, 5, 11, 11, 16, 16, 16, 42, 42, 134, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 349 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478881 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 130, 107, 130, 107, 107, 107, 96, 67, 50, 67, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 107, 134, 134, 201, 201, 201, 201, 201, 134, 107, 107, 107, 107, 107, 96, 96, 67, 67, 67, 28, 28, 1, 107, 107] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 921 number of broken/clashed sets: 105 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478881 none CCC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 27, 41, 107, 107, 107, 107, 107, 1, 4, 4, 13, 13, 13, 12, 12, 5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 27, 27, 107, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478881 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478881 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478881/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478881 Building REAL300025478882 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478882' /scratch/stefan/7787258/working/building/REAL300025478882 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478882 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478882/0 /scratch/stefan/7787258/working/building/REAL300025478882 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/777 `/scratch/stefan/7787258/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025478882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478882 none CCC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 15, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 20, 32, 84, 84, 84, 84, 84, 1, 19, 20, 19, 20, 20, 20, 20, 20, 19, 15, 15, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 20, 20, 84, 1, 1, 20, 20, 20, 20, 19, 20, 20] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 39, 48, 49, 23, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 272 number of broken/clashed sets: 172 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478882 none CCC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 190, 84, 84, 84, 84, 84, 84, 72, 43, 34, 43, 23, 34, 11, 1, 1, 1, 1, 1, 1, 1, 84, 198, 201, 198, 201, 201, 201, 201, 201, 198, 190, 190, 84, 84, 84, 84, 84, 72, 72, 43, 43, 43, 23, 23, 1, 84, 84, 201, 201, 201, 201, 198, 201, 201] 201 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 865 number of broken/clashed sets: 172 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478882 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478882 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478882/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478882 Building REAL300025478883 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478883' /scratch/stefan/7787258/working/building/REAL300025478883 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478883 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478883/0 /scratch/stefan/7787258/working/building/REAL300025478883 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/778 `/scratch/stefan/7787258/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCCC[NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478883 none CN(CC1CCN(C(=O)CCCC[NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 11, 16, 19, 19, 19, 1, 3, 3, 3, 5, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 10, 16, 16, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 7] 19 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 35, 52, 53, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 54, 55, 56]) total number of confs: 131 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478883 none CN(CC1CCN(C(=O)CCCC[NH+](C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 15, 13, 16, 19, 19, 19, 19, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 16, 16, 16, 15, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 1] 19 rigid atoms, others: [56, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478883 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478883 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478883/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478883 Building REAL300025478884 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478884' /scratch/stefan/7787258/working/building/REAL300025478884 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478884 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478884/0 /scratch/stefan/7787258/working/building/REAL300025478884 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/779 `/scratch/stefan/7787258/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478884 none CN(CC1CCN(C(=O)[C@@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 1, 15, 35, 35, 73, 100, 171, 171, 171, 171, 171, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 73, 73, 171] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 466 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478884 none CN(CC1CCN(C(=O)[C@@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 89, 111, 156, 171, 171, 171, 171, 191, 191, 201, 201, 201, 201, 201, 201, 171, 42, 89, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 156, 156, 171, 171, 171, 171, 171, 201, 201, 201, 201, 201, 171, 171, 42, 42, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 783 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478884 none CN(CC1CCN(C(=O)[C@@H]2CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 34, 61, 61, 104, 133, 201, 201, 201, 201, 201, 34, 34, 34, 18, 18, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 104, 104, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46]) total number of confs: 561 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478884 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478884 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478884/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478884 Building REAL300025478885 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478885' /scratch/stefan/7787258/working/building/REAL300025478885 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478885 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478885/0 /scratch/stefan/7787258/working/building/REAL300025478885 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/780 `/scratch/stefan/7787258/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478885 none C[C@H]1CC[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 17, 27, 27, 47, 47, 76, 117, 201, 201, 201, 201, 201, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 27, 27, 27, 76, 76, 201, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 52, 53, 54, 51, 27, 28, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 540 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: REAL300025478885 none C[C@H]1CC[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 134, 201, 122, 134, 122, 122, 122, 104, 73, 51, 73, 26, 51, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 104, 104, 73, 73, 73, 26, 26, 1, 122, 122, 201, 201, 201, 201] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 780 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: REAL300025478885 none C[C@H]1CC[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 40, 64, 122, 122, 122, 122, 122, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 40, 40, 122, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 49, 50, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 322 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478885 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478885 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478885/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478885 Building REAL300025478886 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478886' /scratch/stefan/7787258/working/building/REAL300025478886 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478886 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478886/0 /scratch/stefan/7787258/working/building/REAL300025478886 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/781 `/scratch/stefan/7787258/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478886 none CC(C)C(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 5, 1, 5, 1, 1, 1, 1, 1, 4, 7, 7, 10, 10, 24, 38, 92, 92, 92, 92, 92, 1, 6, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 24, 24, 92, 1, 1, 9, 9, 9, 9, 9, 9] 117 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 39, 40, 50, 23, 4, 49, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 240 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478886 none CC(C)C(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 105, 117, 104, 92, 104, 92, 92, 92, 82, 78, 63, 78, 32, 63, 13, 1, 1, 1, 1, 1, 1, 1, 92, 105, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 105, 92, 92, 92, 92, 92, 82, 82, 78, 78, 78, 32, 32, 1, 92, 92, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [48, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 523 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478886 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478886 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478886/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478886 Building REAL300025478887 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478887' /scratch/stefan/7787258/working/building/REAL300025478887 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478887 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478887/0 /scratch/stefan/7787258/working/building/REAL300025478887 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/782 `/scratch/stefan/7787258/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478887 none CCC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 1, 1] 5 rigid atoms, others: [43, 8, 44, 10, 11, 12, 13, 14, 45, 46, 55, 56, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 25 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478887 none CCC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3] 5 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 16 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478887 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478887/1 /scratch/stefan/7787258/working/building/REAL300025478887 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/783 `/scratch/stefan/7787258/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478887.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478887 none CCC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 1, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 1, 1] 6 rigid atoms, others: [43, 8, 44, 10, 11, 12, 13, 14, 45, 46, 55, 56, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 34 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478887 none CCC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3] 6 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 19 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478887 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478887 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478887/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478887/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478887 Building REAL300025478888 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478888' /scratch/stefan/7787258/working/building/REAL300025478888 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478888 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478888/0 /scratch/stefan/7787258/working/building/REAL300025478888 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/784 `/scratch/stefan/7787258/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478888 none CCC[N@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 17, 13, 7, 13, 13, 3, 1, 3, 1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 15, 27, 108, 108, 108, 108, 108, 1, 23, 23, 23, 23, 23, 17, 17, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 108, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 52, 53, 41, 7, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 293 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478888 none CCC[N@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 181, 197, 197, 111, 108, 111, 108, 108, 108, 73, 65, 56, 65, 34, 56, 13, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 181, 181, 108, 108, 108, 108, 108, 73, 73, 65, 65, 65, 34, 34, 1, 108, 108] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 911 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478888 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478888/1 /scratch/stefan/7787258/working/building/REAL300025478888 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/785 `/scratch/stefan/7787258/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478888.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478888 none CCC[N@@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 12, 12, 3, 1, 3, 1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 15, 28, 109, 109, 109, 109, 109, 1, 22, 22, 22, 22, 22, 16, 16, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 15, 109, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 52, 53, 41, 7, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 290 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478888 none CCC[N@@H+](C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 180, 199, 199, 111, 109, 111, 109, 109, 109, 74, 66, 58, 66, 34, 58, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 180, 180, 109, 109, 109, 109, 109, 74, 74, 66, 66, 66, 34, 34, 1, 109, 109] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 918 number of broken/clashed sets: 156 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478888 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478888 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478888/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478888/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478888 Building REAL300025478889 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478889' /scratch/stefan/7787258/working/building/REAL300025478889 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478889 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478889/0 /scratch/stefan/7787258/working/building/REAL300025478889 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/786 `/scratch/stefan/7787258/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C) `REAL300025478889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478889 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 10, 10, 24, 41, 95, 95, 95, 95, 95, 1, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 24, 24, 95, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 46, 47, 35, 22, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 264 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478889 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 102, 95, 102, 95, 95, 95, 81, 60, 44, 60, 24, 44, 12, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 95, 95, 95, 81, 81, 60, 60, 60, 24, 24, 1, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 881 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478889 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478889 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478889/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478889 Building REAL300025478890 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478890' /scratch/stefan/7787258/working/building/REAL300025478890 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478890 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478890/0 /scratch/stefan/7787258/working/building/REAL300025478890 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/787 `/scratch/stefan/7787258/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1) `REAL300025478890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478890 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 13, 13, 20, 20, 20, 20, 41, 53, 53, 55, 55, 82, 114, 201, 201, 201, 201, 201, 20, 1, 1, 1, 2, 2, 2, 4, 4, 20, 20, 20, 20, 20, 41, 41, 53, 53, 53, 82, 82, 201, 20, 20, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 580 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478890 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 106, 116, 106, 106, 106, 91, 64, 42, 64, 25, 42, 13, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106, 106, 106, 106, 91, 91, 64, 64, 64, 25, 25, 1, 106, 106, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 836 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478890 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 23, 34, 106, 106, 106, 106, 106, 1, 20, 20, 20, 20, 20, 20, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 106, 1, 1, 20, 20] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 269 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478890 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478890 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478890/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478890 Building REAL300025478891 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478891' /scratch/stefan/7787258/working/building/REAL300025478891 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478891 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478891/0 /scratch/stefan/7787258/working/building/REAL300025478891 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/788 `/scratch/stefan/7787258/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1) `REAL300025478891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478891 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 18, 22, 22, 23, 23, 46, 69, 143, 143, 143, 143, 143, 9, 1, 1, 1, 6, 6, 6, 5, 5, 9, 9, 9, 9, 9, 18, 18, 22, 22, 22, 46, 46, 143, 9, 9, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 379 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478891 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 143, 105, 96, 105, 96, 96, 96, 70, 46, 40, 46, 27, 40, 13, 1, 1, 1, 1, 1, 1, 1, 96, 143, 143, 143, 201, 201, 201, 201, 201, 96, 96, 96, 96, 96, 70, 70, 46, 46, 46, 27, 27, 1, 96, 96, 143, 143] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 820 number of broken/clashed sets: 147 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478891 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 20, 32, 96, 96, 96, 96, 96, 1, 9, 9, 9, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 20, 20, 96, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 254 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478891 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478891 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478891/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478891 Building REAL300025478892 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478892' /scratch/stefan/7787258/working/building/REAL300025478892 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478892 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478892/0 /scratch/stefan/7787258/working/building/REAL300025478892 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/789 `/scratch/stefan/7787258/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478892 none CC1=NNC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 18, 27, 27, 50, 50, 80, 119, 201, 201, 201, 201, 201, 6, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 18, 18, 27, 27, 27, 80, 80, 201, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 561 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: REAL300025478892 none CC1=NNC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 153, 201, 153, 153, 153, 140, 93, 61, 93, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 140, 140, 93, 93, 93, 29, 29, 1, 153, 153] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 780 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: REAL300025478892 none CC1=NNC(C)=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 6, 13, 13, 31, 31, 54, 84, 153, 153, 153, 153, 153, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 54, 54, 153, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478892 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478892 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478892/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478892 Building REAL300025478893 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478893' /scratch/stefan/7787258/working/building/REAL300025478893 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478893 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478893/0 /scratch/stefan/7787258/working/building/REAL300025478893 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/790 `/scratch/stefan/7787258/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478893 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 25, 38, 38, 56, 56, 81, 122, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 38, 38, 38, 81, 81, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 562 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: REAL300025478893 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 158, 138, 158, 138, 138, 138, 118, 87, 64, 87, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 118, 118, 87, 87, 87, 29, 29, 1, 138, 138] 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, 46, 47]) total number of confs: 677 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: REAL300025478893 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 23, 23, 42, 63, 138, 138, 138, 138, 138, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 42, 42, 138, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478893 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478893 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478893/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478893 Building REAL300025478894 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478894' /scratch/stefan/7787258/working/building/REAL300025478894 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478894 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478894/0 /scratch/stefan/7787258/working/building/REAL300025478894 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/791 `/scratch/stefan/7787258/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478894 none CC(C)CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 14, 14, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 22, 36, 104, 104, 104, 104, 104, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 15, 15, 14, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 22, 22, 104, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 271 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478894 none CC(C)CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 196, 113, 104, 113, 104, 104, 104, 89, 68, 47, 68, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 196, 196, 104, 104, 104, 104, 104, 89, 89, 68, 68, 68, 28, 28, 1, 104, 104] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 873 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478894 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478894 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478894/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478894 Building REAL300025478895 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478895' /scratch/stefan/7787258/working/building/REAL300025478895 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478895 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478895/0 /scratch/stefan/7787258/working/building/REAL300025478895 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/792 `/scratch/stefan/7787258/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478895 none CN(CC1CCN(C(=O)CCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 1, 8, 12, 12, 16, 16, 39, 39, 39, 39, 39, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 16, 16, 39] 75 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 49, 50, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478895 none CN(CC1CCN(C(=O)CCC(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [31, 30, 31, 34, 39, 39, 39, 39, 46, 46, 75, 75, 75, 75, 75, 39, 26, 30, 12, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 34, 34, 39, 39, 39, 39, 39, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 39, 39, 26, 26, 1] 75 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 318 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478895 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478895 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478895/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478895 Building REAL300025478896 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478896' /scratch/stefan/7787258/working/building/REAL300025478896 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478896 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478896/0 /scratch/stefan/7787258/working/building/REAL300025478896 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/793 `/scratch/stefan/7787258/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478896 none CN(CC1CCN(C(=O)C2=CC=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1, 13, 30, 30, 57, 83, 155, 155, 155, 155, 155, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 57, 57, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 397 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478896 none CN(CC1CCN(C(=O)C2=CC=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 62, 81, 132, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 155, 32, 62, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 132, 132, 155, 155, 155, 155, 155, 201, 201, 201, 155, 155, 32, 32, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 819 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478896 none CN(CC1CCN(C(=O)C2=CC=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 18, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 32, 63, 63, 111, 145, 201, 201, 201, 201, 201, 32, 32, 32, 18, 18, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 111, 111, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 610 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478896 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478896 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478896/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478896 Building REAL300025478897 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478897' /scratch/stefan/7787258/working/building/REAL300025478897 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478897 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478897/0 /scratch/stefan/7787258/working/building/REAL300025478897 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/794 `/scratch/stefan/7787258/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1) `REAL300025478897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478897 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 33, 43, 43, 52, 52, 81, 120, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 13, 33, 33, 43, 43, 43, 81, 81, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 46, 47, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 564 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478897 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 103, 114, 103, 103, 103, 88, 69, 49, 69, 28, 49, 12, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 191, 201, 201, 201, 201, 103, 103, 103, 103, 103, 88, 88, 69, 69, 69, 28, 28, 1, 103, 103, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 627 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478897 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 29, 43, 103, 103, 103, 103, 103, 1, 13, 13, 5, 13, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 29, 29, 103, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 271 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478897 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478897 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478897/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478897 Building REAL300025478898 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478898' /scratch/stefan/7787258/working/building/REAL300025478898 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478898 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478898/0 /scratch/stefan/7787258/working/building/REAL300025478898 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/795 `/scratch/stefan/7787258/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478898 none CN(CC1CCN(C(=O)CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 18, 33, 33, 33, 33, 1, 8, 13, 13, 20, 21, 44, 44, 44, 44, 44, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 18, 18, 33, 33, 33, 1, 1, 20, 20, 44] 109 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478898 none CN(CC1CCN(C(=O)CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [36, 35, 36, 41, 44, 44, 44, 44, 60, 60, 97, 109, 109, 109, 109, 44, 28, 35, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 41, 41, 44, 44, 44, 44, 44, 97, 97, 109, 109, 109, 44, 44, 28, 28, 1] 109 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: 435 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478898 none CN(CC1CCN(C(=O)CC2=CC=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [60, 49, 33, 33, 33, 33, 18, 5, 18, 1, 1, 1, 1, 1, 1, 33, 60, 71, 71, 82, 82, 109, 109, 109, 109, 109, 60, 60, 60, 49, 49, 33, 33, 33, 33, 33, 5, 5, 1, 1, 1, 33, 33, 82, 82, 109] 109 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 343 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478898 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478898 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478898/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478898 Building REAL300025478899 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478899' /scratch/stefan/7787258/working/building/REAL300025478899 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478899 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478899/0 /scratch/stefan/7787258/working/building/REAL300025478899 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/796 `/scratch/stefan/7787258/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478899 none CN(CC1CCN(C(=O)C2=NC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 3, 9, 9, 1, 12, 36, 36, 68, 98, 172, 172, 172, 172, 172, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 9, 3, 9, 1, 1, 68, 68, 172] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 461 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478899 none CN(CC1CCN(C(=O)C2=NC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 87, 111, 157, 172, 172, 172, 172, 182, 182, 201, 201, 182, 201, 201, 172, 36, 87, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 157, 157, 172, 172, 172, 172, 172, 201, 182, 201, 172, 172, 36, 36, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 796 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478899 none CN(CC1CCN(C(=O)C2=NC=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 27, 48, 48, 71, 92, 134, 134, 134, 134, 134, 27, 27, 27, 19, 19, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 71, 71, 134] 134 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 402 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478899 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478899 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478899/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478899 Building REAL300025478900 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478900' /scratch/stefan/7787258/working/building/REAL300025478900 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478900 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478900/0 /scratch/stefan/7787258/working/building/REAL300025478900 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/797 `/scratch/stefan/7787258/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478900 none CCC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 17, 27, 71, 71, 71, 71, 71, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 17, 17, 71, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 241 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478900 none CCC(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 201, 127, 71, 71, 71, 71, 71, 71, 64, 43, 33, 43, 23, 33, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 71, 71, 71, 71, 71, 64, 64, 43, 43, 43, 23, 23, 1, 71, 71] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 998 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478900 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478900 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478900/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478900 Building REAL300025478901 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478901' /scratch/stefan/7787258/working/building/REAL300025478901 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478901 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478901/0 /scratch/stefan/7787258/working/building/REAL300025478901 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/798 `/scratch/stefan/7787258/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478901 none CN(CC1CCN(C(=O)C2=CC=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 9, 10, 10, 10, 1, 13, 30, 30, 52, 77, 151, 151, 151, 151, 151, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 52, 52, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 382 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: REAL300025478901 none CN(CC1CCN(C(=O)C2=CC=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 72, 88, 136, 151, 151, 151, 151, 198, 198, 201, 201, 201, 201, 201, 151, 35, 72, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 136, 136, 151, 151, 151, 151, 151, 201, 201, 201, 151, 151, 35, 35, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 807 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: REAL300025478901 none CN(CC1CCN(C(=O)C2=CC=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 40, 71, 71, 114, 154, 201, 201, 201, 201, 201, 40, 40, 40, 24, 24, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 114, 114, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 607 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478901 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478901 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478901/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478901 Building REAL300025478902 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478902' /scratch/stefan/7787258/working/building/REAL300025478902 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478902 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478902/0 /scratch/stefan/7787258/working/building/REAL300025478902 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/799 `/scratch/stefan/7787258/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478902 none COC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 19, 30, 30, 40, 40, 73, 111, 201, 201, 201, 201, 201, 7, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 19, 19, 30, 30, 30, 73, 73, 201, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 529 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478902 none COC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 196, 185, 196, 185, 185, 185, 170, 114, 68, 114, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185, 185, 170, 170, 114, 114, 114, 29, 29, 1, 185, 185] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 752 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478902 none COC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 52, 84, 185, 185, 185, 185, 185, 1, 7, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 52, 52, 185, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 437 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478902 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478902 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478902/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478902 Building REAL300025478903 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478903' /scratch/stefan/7787258/working/building/REAL300025478903 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478903 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478903/0 /scratch/stefan/7787258/working/building/REAL300025478903 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/800 `/scratch/stefan/7787258/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1) `REAL300025478903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478903 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 7, 8, 8, 8, 21, 34, 34, 52, 52, 77, 119, 201, 201, 201, 201, 201, 7, 1, 1, 1, 2, 2, 2, 7, 7, 8, 8, 8, 21, 21, 34, 34, 34, 77, 77, 201, 7, 7, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 539 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: REAL300025478903 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 160, 190, 160, 160, 160, 145, 98, 59, 98, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 145, 145, 98, 98, 98, 30, 30, 1, 160, 160, 201, 201, 201] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 746 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: REAL300025478903 none CC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 30, 30, 51, 80, 160, 160, 160, 160, 160, 1, 7, 7, 7, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 51, 51, 160, 1, 1, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 389 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478903 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478903 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478903/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478903 Building REAL300025478904 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478904' /scratch/stefan/7787258/working/building/REAL300025478904 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478904 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478904/0 /scratch/stefan/7787258/working/building/REAL300025478904 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/801 `/scratch/stefan/7787258/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478904 none CN(CC1CCN(C(=O)CCN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 19, 26, 46, 46, 46, 46, 1, 11, 16, 16, 22, 22, 45, 45, 45, 45, 45, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 19, 19, 26, 26, 46, 1, 1, 22, 22, 45] 136 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478904 none CN(CC1CCN(C(=O)CCN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [38, 37, 38, 40, 45, 45, 45, 45, 62, 62, 121, 132, 136, 136, 136, 136, 45, 28, 37, 13, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 40, 40, 45, 45, 45, 45, 45, 121, 121, 132, 132, 136, 45, 45, 28, 28, 1] 136 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 565 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478904 none CN(CC1CCN(C(=O)CCN2C=NN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [83, 66, 46, 46, 46, 46, 31, 14, 31, 8, 1, 1, 1, 1, 1, 1, 46, 83, 97, 97, 108, 108, 136, 136, 136, 136, 136, 83, 83, 83, 66, 66, 46, 46, 46, 46, 46, 14, 14, 8, 8, 1, 46, 46, 108, 108, 136] 136 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 460 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478904 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478904 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478904/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478904 Building REAL300025478905 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478905' /scratch/stefan/7787258/working/building/REAL300025478905 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478905 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478905/0 /scratch/stefan/7787258/working/building/REAL300025478905 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/802 `/scratch/stefan/7787258/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478905 none CN(CC1CCN(C(=O)C2=NC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 11, 11, 1, 12, 31, 31, 58, 83, 145, 145, 145, 145, 145, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 58, 58, 145] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 388 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: REAL300025478905 none CN(CC1CCN(C(=O)C2=NC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 80, 97, 131, 145, 145, 145, 145, 158, 158, 201, 201, 201, 201, 201, 201, 145, 33, 80, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 131, 131, 145, 145, 145, 145, 145, 201, 201, 201, 145, 145, 33, 33, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 689 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: REAL300025478905 none CN(CC1CCN(C(=O)C2=NC=CC=C2F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 27, 12, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 11, 39, 75, 75, 117, 146, 201, 201, 201, 201, 201, 39, 39, 39, 27, 27, 12, 11, 12, 12, 12, 1, 1, 1, 12, 12, 117, 117, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 627 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478905 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478905 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478905/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478905 Building REAL300025478906 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478906' /scratch/stefan/7787258/working/building/REAL300025478906 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478906 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478906/0 /scratch/stefan/7787258/working/building/REAL300025478906 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/803 `/scratch/stefan/7787258/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478906 none CC1OCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 10, 19, 19, 47, 47, 79, 120, 201, 201, 201, 201, 201, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 19, 19, 19, 79, 79, 201, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 518 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: REAL300025478906 none CC1OCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 185, 201, 185, 185, 185, 177, 119, 68, 119, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185, 185, 177, 177, 119, 119, 119, 29, 29, 1, 185, 185] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 764 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: REAL300025478906 none CC1OCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 6, 14, 14, 39, 39, 71, 107, 185, 185, 185, 185, 185, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 71, 71, 185, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 470 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478906 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478906 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478906/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478906 Building REAL300025478907 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478907' /scratch/stefan/7787258/working/building/REAL300025478907 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478907 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478907/0 /scratch/stefan/7787258/working/building/REAL300025478907 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/804 `/scratch/stefan/7787258/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478907 none CN(CC1CCN(C(=O)C2(C)CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 15, 36, 36, 74, 102, 153, 153, 153, 153, 153, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 74, 74, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 439 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478907 none CN(CC1CCN(C(=O)C2(C)CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 64, 86, 129, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 153, 35, 64, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 129, 129, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 35, 35, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 802 number of broken/clashed sets: 99 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478907 none CN(CC1CCN(C(=O)C2(C)CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 28, 57, 57, 106, 146, 201, 201, 201, 201, 201, 28, 28, 28, 13, 13, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 106, 106, 201] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49]) total number of confs: 603 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478907 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478907 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478907/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478907 Building REAL300025478908 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478908' /scratch/stefan/7787258/working/building/REAL300025478908 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478908 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478908/0 /scratch/stefan/7787258/working/building/REAL300025478908 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/805 `/scratch/stefan/7787258/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478908 none CCC(CC)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 5, 5, 1, 3, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 25, 48, 112, 112, 112, 112, 112, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 25, 25, 112, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 278 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478908 none CCC(CC)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 146, 173, 201, 173, 173, 112, 146, 112, 112, 112, 92, 51, 51, 51, 27, 51, 12, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 173, 173, 112, 112, 112, 112, 112, 92, 92, 51, 51, 51, 27, 27, 1, 112, 112] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 1075 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478908 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478908 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478908/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478908 Building REAL300025478909 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478909' /scratch/stefan/7787258/working/building/REAL300025478909 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478909 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478909/0 /scratch/stefan/7787258/working/building/REAL300025478909 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/806 `/scratch/stefan/7787258/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1) `REAL300025478909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478909 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 20, 30, 30, 45, 45, 76, 112, 201, 201, 201, 201, 201, 7, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 30, 30, 30, 76, 76, 201, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 49, 50, 51, 52, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 543 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478909 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 128, 137, 128, 128, 128, 108, 79, 60, 79, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 108, 108, 79, 79, 79, 28, 28, 1, 128, 128, 201, 201, 201, 201] 201 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 785 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478909 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 39, 61, 128, 128, 128, 128, 128, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 39, 39, 128, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 47, 48, 23, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 321 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478909 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478909 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478909/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478909 Building REAL300025478910 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478910' /scratch/stefan/7787258/working/building/REAL300025478910 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478910 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478910/0 /scratch/stefan/7787258/working/building/REAL300025478910 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/807 `/scratch/stefan/7787258/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478910 none CCCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 9, 5, 9, 9, 12, 1, 5, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 9, 15, 60, 60, 60, 60, 60, 1, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 9, 9, 60, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478910 none CCCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 148, 92, 148, 148, 158, 60, 92, 60, 60, 60, 60, 57, 56, 57, 30, 56, 12, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 158, 158, 158, 158, 158, 60, 60, 60, 60, 60, 60, 60, 57, 57, 57, 30, 30, 1, 60, 60] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 981 number of broken/clashed sets: 197 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478910 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478910 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478910/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478910 Building REAL300025478911 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478911' /scratch/stefan/7787258/working/building/REAL300025478911 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478911 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478911/0 /scratch/stefan/7787258/working/building/REAL300025478911 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/808 `/scratch/stefan/7787258/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478911 none CCC(CC)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 17, 17, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 19, 29, 84, 84, 84, 84, 84, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 19, 19, 84, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478911 none CCC(CC)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 201, 201, 90, 84, 90, 84, 84, 84, 73, 46, 36, 46, 24, 36, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 84, 84, 84, 84, 84, 73, 73, 46, 46, 46, 24, 24, 1, 84, 84] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 850 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478911 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478911 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478911/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478911 Building REAL300025478912 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478912' /scratch/stefan/7787258/working/building/REAL300025478912 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478912 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478912/0 /scratch/stefan/7787258/working/building/REAL300025478912 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/809 `/scratch/stefan/7787258/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478912 none CCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 6, 12, 12, 23, 23, 50, 82, 189, 189, 189, 189, 189, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 50, 50, 189, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 439 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478912 none CCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 201, 189, 198, 189, 189, 189, 171, 115, 71, 115, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 189, 189, 171, 171, 115, 115, 115, 30, 30, 1, 189, 189] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 752 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478912 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478912 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478912/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478912 Building REAL300025478913 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478913' /scratch/stefan/7787258/working/building/REAL300025478913 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478913 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478913/0 /scratch/stefan/7787258/working/building/REAL300025478913 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/810 `/scratch/stefan/7787258/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478913 none CCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 40, 67, 151, 151, 151, 151, 151, 1, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 40, 40, 151, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 374 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478913 none CCCC(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 163, 200, 200, 151, 163, 151, 151, 151, 136, 92, 57, 92, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 200, 151, 151, 151, 151, 151, 136, 136, 92, 92, 92, 27, 27, 1, 151, 151] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 835 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478913 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478913 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478913/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478913 Building REAL300025478914 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478914' /scratch/stefan/7787258/working/building/REAL300025478914 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478914 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478914/0 /scratch/stefan/7787258/working/building/REAL300025478914 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/811 `/scratch/stefan/7787258/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(=O)NCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478914 none CN(CC1CCN(C(=O)C(=O)NCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 9, 25, 42, 42, 1, 7, 8, 8, 10, 10, 22, 22, 22, 22, 22, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 8, 25, 25, 42, 42, 42, 42, 42, 1, 1, 10, 10, 22] 85 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 199 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: REAL300025478914 none CN(CC1CCN(C(=O)C(=O)NCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 22, 22, 22, 22, 35, 35, 53, 53, 53, 81, 85, 85, 22, 18, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 53, 81, 81, 85, 85, 85, 85, 85, 22, 22, 18, 18, 1] 85 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 330 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: REAL300025478914 none CN(CC1CCN(C(=O)C(=O)NCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 53, 42, 42, 42, 42, 29, 14, 32, 14, 14, 6, 1, 1, 1, 1, 42, 63, 66, 66, 74, 74, 85, 85, 85, 85, 85, 63, 63, 63, 53, 53, 42, 42, 42, 42, 42, 14, 6, 6, 1, 1, 1, 1, 1, 42, 42, 74, 74, 85] 85 rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 44] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49]) total number of confs: 301 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478914 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478914 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478914/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478914 Building REAL300025478915 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478915' /scratch/stefan/7787258/working/building/REAL300025478915 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478915 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478915/0 /scratch/stefan/7787258/working/building/REAL300025478915 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/812 `/scratch/stefan/7787258/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478915 none CN(CC1CCN(C(=O)C2(C)CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 13, 29, 29, 57, 78, 131, 131, 131, 131, 131, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 57, 57, 131] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 371 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478915 none CN(CC1CCN(C(=O)C2(C)CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 69, 91, 117, 131, 131, 131, 131, 164, 164, 201, 201, 201, 201, 201, 201, 131, 35, 69, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 117, 117, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 35, 35, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 791 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478915 none CN(CC1CCN(C(=O)C2(C)CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 15, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 29, 65, 65, 107, 144, 201, 201, 201, 201, 201, 29, 29, 29, 15, 15, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 107, 107, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52]) total number of confs: 602 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478915 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478915 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478915/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478915 Building REAL300025478916 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478916' /scratch/stefan/7787258/working/building/REAL300025478916 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478916 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478916/0 /scratch/stefan/7787258/working/building/REAL300025478916 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/813 `/scratch/stefan/7787258/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1) `REAL300025478916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478916 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 11, 16, 16, 22, 22, 41, 62, 123, 123, 123, 123, 123, 4, 1, 1, 6, 6, 6, 6, 6, 1, 4, 4, 4, 4, 4, 11, 11, 16, 16, 16, 41, 41, 123, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 338 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478916 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 121, 94, 121, 94, 94, 94, 85, 63, 48, 63, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 94, 123, 123, 201, 201, 201, 201, 201, 123, 94, 94, 94, 94, 94, 85, 85, 63, 63, 63, 28, 28, 1, 94, 94] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 941 number of broken/clashed sets: 97 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478916 none CCN1C=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 26, 39, 94, 94, 94, 94, 94, 1, 4, 4, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 26, 26, 94, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478916 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478916 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478916/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478916 Building REAL300025478917 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478917' /scratch/stefan/7787258/working/building/REAL300025478917 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478917 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478917/0 /scratch/stefan/7787258/working/building/REAL300025478917 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/814 `/scratch/stefan/7787258/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478917 none CCC1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 19, 29, 29, 42, 42, 72, 117, 201, 201, 201, 201, 201, 7, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 29, 29, 29, 72, 72, 201, 7, 7] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 2, 35, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 537 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: REAL300025478917 none CCC1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 173, 159, 173, 159, 159, 159, 135, 90, 58, 90, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 135, 135, 90, 90, 90, 28, 28, 1, 159, 159] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 770 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: REAL300025478917 none CCC1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 46, 75, 159, 159, 159, 159, 159, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 46, 46, 159, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 403 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478917 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478917 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478917/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478917 Building REAL300025478918 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478918' /scratch/stefan/7787258/working/building/REAL300025478918 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478918 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478918/0 /scratch/stefan/7787258/working/building/REAL300025478918 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/815 `/scratch/stefan/7787258/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478918 none CC(C)C1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 18, 27, 27, 40, 40, 69, 114, 201, 201, 201, 201, 201, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 27, 27, 27, 69, 69, 201, 7, 7] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 534 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: REAL300025478918 none CC(C)C1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 156, 169, 156, 156, 156, 132, 84, 54, 84, 22, 54, 12, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 132, 132, 84, 84, 84, 22, 22, 1, 156, 156] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 781 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: REAL300025478918 none CC(C)C1(C)CC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 46, 76, 156, 156, 156, 156, 156, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 46, 46, 156, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 393 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478918 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478918 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478918/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478918 Building REAL300025478919 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478919' /scratch/stefan/7787258/working/building/REAL300025478919 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478919 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478919/0 /scratch/stefan/7787258/working/building/REAL300025478919 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/816 `/scratch/stefan/7787258/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478919 none COCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 23, 14, 23, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 17, 17, 24, 30, 66, 66, 66, 66, 66, 1, 53, 53, 53, 39, 39, 23, 23, 23, 23, 14, 14, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 24, 24, 66, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 382 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478919 none COCC(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 165, 157, 165, 74, 66, 74, 66, 66, 66, 56, 47, 35, 47, 16, 35, 12, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 165, 165, 165, 165, 157, 157, 66, 66, 66, 66, 66, 56, 56, 47, 47, 47, 16, 16, 1, 66, 66] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 857 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478919 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478919 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478919/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478919 Building REAL300025478920 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478920' /scratch/stefan/7787258/working/building/REAL300025478920 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478920 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478920/0 /scratch/stefan/7787258/working/building/REAL300025478920 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/817 `/scratch/stefan/7787258/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478920 none COCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 10, 6, 10, 10, 1, 6, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 10, 17, 69, 69, 69, 69, 69, 1, 43, 43, 43, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 10, 10, 69, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 234 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478920 none COCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 111, 170, 170, 69, 111, 69, 69, 69, 69, 64, 57, 64, 31, 57, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 170, 69, 69, 69, 69, 69, 69, 69, 64, 64, 64, 31, 31, 1, 69, 69] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 916 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478920 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478920 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478920/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478920 Building REAL300025478921 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478921' /scratch/stefan/7787258/working/building/REAL300025478921 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478921 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478921/0 /scratch/stefan/7787258/working/building/REAL300025478921 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/818 `/scratch/stefan/7787258/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1) `REAL300025478921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478921 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 3, 3, 5, 5, 5, 5, 9, 18, 18, 42, 42, 72, 113, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 9, 9, 18, 18, 18, 72, 72, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 47, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 510 number of broken/clashed sets: 196 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478921 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 192, 199, 192, 192, 192, 173, 121, 68, 121, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 192, 192, 192, 173, 173, 121, 121, 121, 29, 29, 1, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 754 number of broken/clashed sets: 196 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478921 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 1, 1, 1, 1, 6, 15, 15, 39, 39, 69, 108, 192, 192, 192, 192, 192, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 69, 69, 192, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 45, 46, 35, 22] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 495 number of broken/clashed sets: 196 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478921 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478921 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478921/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478921 Building REAL300025478922 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478922' /scratch/stefan/7787258/working/building/REAL300025478922 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478922 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478922/0 /scratch/stefan/7787258/working/building/REAL300025478922 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/819 `/scratch/stefan/7787258/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NON=C1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478922 none CC1=NON=C1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 13, 13, 13, 13, 29, 37, 37, 51, 51, 79, 119, 201, 201, 201, 201, 201, 13, 2, 2, 2, 3, 3, 13, 13, 13, 13, 13, 29, 29, 37, 37, 37, 79, 79, 201, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 549 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478922 none CC1=NON=C1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 117, 142, 117, 117, 117, 107, 80, 55, 80, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 117, 117, 117, 117, 117, 107, 107, 80, 80, 80, 27, 27, 1, 117, 117] 201 rigid atoms, others: [44, 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, 45, 46]) total number of confs: 817 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478922 none CC1=NON=C1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 19, 19, 36, 58, 117, 117, 117, 117, 117, 1, 13, 13, 13, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 36, 36, 117, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 9, 10, 11, 12, 13, 46, 45, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 315 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478922 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478922 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478922/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478922 Building REAL300025478923 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478923' /scratch/stefan/7787258/working/building/REAL300025478923 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478923 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478923/0 /scratch/stefan/7787258/working/building/REAL300025478923 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/820 `/scratch/stefan/7787258/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)COC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478923 none CN(CC1CCN(C(=O)COC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 3, 3, 12, 29, 41, 41, 41, 41, 1, 10, 14, 14, 21, 21, 49, 49, 49, 49, 49, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 41, 41, 1, 1, 21, 21, 49] 193 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478923 none CN(CC1CCN(C(=O)COC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 41, 45, 49, 49, 49, 49, 60, 60, 109, 155, 193, 193, 193, 193, 49, 28, 39, 13, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 45, 45, 49, 49, 49, 49, 49, 109, 109, 193, 193, 193, 193, 193, 193, 193, 49, 49, 28, 28, 1] 193 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 686 number of broken/clashed sets: 107 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478923 none CN(CC1CCN(C(=O)COC2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [98, 67, 41, 41, 41, 41, 31, 15, 31, 5, 1, 1, 1, 1, 1, 1, 41, 98, 122, 122, 138, 138, 193, 193, 193, 193, 193, 98, 98, 98, 67, 67, 41, 41, 41, 41, 41, 15, 15, 1, 1, 1, 1, 1, 1, 1, 41, 41, 138, 138, 193] 193 rigid atoms, others: [45, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50]) total number of confs: 641 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478923 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478923 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478923/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478923 Building REAL300025478924 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478924' /scratch/stefan/7787258/working/building/REAL300025478924 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478924 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478924/0 /scratch/stefan/7787258/working/building/REAL300025478924 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/821 `/scratch/stefan/7787258/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O) `REAL300025478924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478924 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 11, 11, 19, 19, 41, 68, 153, 153, 153, 153, 153, 1, 11, 15, 15, 15, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 41, 41, 153, 1, 1, 15, 15, 15] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 7, 8, 9, 46, 47, 35, 22, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 415 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478924 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 183, 153, 183, 153, 153, 153, 118, 86, 56, 86, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 118, 118, 86, 86, 86, 29, 29, 1, 153, 153, 201, 201, 201] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50]) total number of confs: 786 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478924 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478924 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478924/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478924 Building REAL300025478925 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478925' /scratch/stefan/7787258/working/building/REAL300025478925 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478925 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478925/0 /scratch/stefan/7787258/working/building/REAL300025478925 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/822 `/scratch/stefan/7787258/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C(F)F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478925 none CN(CC1CCN(C(=O)C2(C(F)F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 8, 12, 12, 8, 8, 1, 5, 7, 7, 8, 8, 12, 12, 12, 12, 12, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 12, 8, 8, 8, 8, 1, 1, 8, 8, 12] 26 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 79 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: REAL300025478925 none CN(CC1CCN(C(=O)C2(C(F)F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 12, 12, 12, 12, 21, 21, 25, 26, 26, 25, 25, 12, 10, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 26, 25, 25, 25, 25, 12, 12, 10, 10, 1] 26 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: 80 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: REAL300025478925 none CN(CC1CCN(C(=O)C2(C(F)F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 8, 8, 8, 8, 3, 1, 3, 1, 1, 7, 7, 1, 1, 8, 15, 19, 19, 21, 21, 25, 25, 25, 25, 25, 15, 15, 15, 12, 12, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 8, 8, 21, 21, 25] 26 rigid atoms, others: [37, 38, 7, 40, 9, 10, 39, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 15, 16, 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]) total number of confs: 103 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478925 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478925 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478925/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478925 Building REAL300025478926 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478926' /scratch/stefan/7787258/working/building/REAL300025478926 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478926 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478926/0 /scratch/stefan/7787258/working/building/REAL300025478926 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/823 `/scratch/stefan/7787258/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478926 none CN(CC1CCN(C(=O)C2CCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 1, 13, 29, 29, 57, 76, 135, 135, 135, 135, 135, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 57, 57, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 361 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478926 none CN(CC1CCN(C(=O)C2CCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 122, 135, 135, 135, 135, 137, 137, 201, 201, 201, 201, 201, 135, 38, 81, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 122, 122, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 38, 38, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 788 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478926 none CN(CC1CCN(C(=O)C2CCC(F)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 34, 65, 65, 107, 137, 201, 201, 201, 201, 201, 34, 34, 34, 21, 21, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 107, 107, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48]) total number of confs: 593 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478926 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478926 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478926/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478926 Building REAL300025478927 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478927' /scratch/stefan/7787258/working/building/REAL300025478927 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478927 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478927/0 /scratch/stefan/7787258/working/building/REAL300025478927 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/824 `/scratch/stefan/7787258/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C[NH+](C)C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478927 none CN(CC1CCN(C(=O)C2(C[NH+](C)C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 5, 5, 1, 9, 14, 14, 18, 20, 24, 24, 24, 24, 24, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 1, 1, 18, 18, 24] 25 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 98 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: REAL300025478927 none CN(CC1CCN(C(=O)C2(C[NH+](C)C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 23, 23, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 17, 21, 11, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 17, 17, 1] 25 rigid atoms, others: [54, 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, 19, 20, 28, 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: 80 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: REAL300025478927 none CN(CC1CCN(C(=O)C2(C[NH+](C)C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 5, 5, 5, 5, 3, 1, 3, 1, 1, 5, 5, 5, 5, 1, 1, 5, 13, 20, 20, 23, 24, 25, 25, 25, 25, 25, 13, 13, 13, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 23, 23, 25] 25 rigid atoms, others: [48, 7, 9, 10, 46, 15, 16, 49, 47] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478927 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478927 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478927/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478927 Building REAL300025478928 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478928' /scratch/stefan/7787258/working/building/REAL300025478928 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478928 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478928/0 /scratch/stefan/7787258/working/building/REAL300025478928 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/825 `/scratch/stefan/7787258/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNC(=O)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478928 none CN(CC1CCN(C(=O)C2=CNC(=O)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 1, 14, 34, 34, 59, 85, 151, 151, 151, 151, 151, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 59, 59, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 396 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478928 none CN(CC1CCN(C(=O)C2=CNC(=O)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 72, 83, 132, 151, 151, 151, 151, 189, 189, 201, 201, 201, 201, 201, 201, 151, 36, 72, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 132, 132, 151, 151, 151, 151, 151, 201, 201, 201, 151, 151, 36, 36, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 781 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478928 none CN(CC1CCN(C(=O)C2=CNC(=O)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 26, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 43, 71, 71, 108, 144, 201, 201, 201, 201, 201, 43, 43, 43, 26, 26, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 108, 108, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 596 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478928 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478928 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478928/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478928 Building REAL300025478929 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478929' /scratch/stefan/7787258/working/building/REAL300025478929 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478929 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478929/0 /scratch/stefan/7787258/working/building/REAL300025478929 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/826 `/scratch/stefan/7787258/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478929 none CCCC(CCC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 7, 3, 7, 13, 14, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 21, 21, 37, 50, 87, 87, 87, 87, 87, 1, 14, 14, 14, 14, 14, 14, 14, 7, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 37, 37, 87, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 342 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478929 none CCCC(CCC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 173, 98, 173, 190, 190, 87, 98, 87, 87, 87, 70, 47, 29, 47, 15, 29, 10, 1, 1, 1, 1, 1, 1, 1, 87, 191, 191, 191, 191, 191, 191, 191, 173, 190, 190, 190, 190, 190, 190, 190, 87, 87, 87, 87, 87, 70, 70, 47, 47, 47, 15, 15, 1, 87, 87] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 942 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478929 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478929 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478929/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478929 Building REAL300025478930 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478930' /scratch/stefan/7787258/working/building/REAL300025478930 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478930 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478930/0 /scratch/stefan/7787258/working/building/REAL300025478930 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/827 `/scratch/stefan/7787258/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478930 none CN(CC1CCN(C(=O)CCC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 19, 21, 31, 31, 31, 1, 8, 12, 12, 17, 18, 42, 42, 42, 42, 42, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 20, 19, 21, 21, 31, 31, 31, 31, 31, 31, 31, 1, 1, 17, 17, 42] 115 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 217 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478930 none CN(CC1CCN(C(=O)CCC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [35, 33, 35, 38, 42, 42, 42, 42, 53, 53, 96, 97, 115, 115, 115, 42, 29, 33, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 38, 38, 42, 42, 42, 42, 42, 96, 96, 98, 98, 115, 115, 115, 115, 115, 115, 115, 42, 42, 29, 29, 1] 115 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 483 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478930 none CN(CC1CCN(C(=O)CCC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [68, 46, 31, 31, 31, 31, 19, 6, 19, 4, 1, 1, 1, 1, 1, 31, 68, 84, 84, 92, 92, 115, 115, 115, 115, 115, 68, 68, 68, 46, 46, 31, 31, 31, 31, 31, 6, 6, 4, 4, 2, 2, 2, 1, 1, 1, 1, 31, 31, 92, 92, 115] 115 rigid atoms, others: [11, 44, 10, 43, 12, 13, 14, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51]) total number of confs: 387 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478930 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478930 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478930/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478930 Building REAL300025478931 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478931' /scratch/stefan/7787258/working/building/REAL300025478931 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478931 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478931/0 /scratch/stefan/7787258/working/building/REAL300025478931 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/828 `/scratch/stefan/7787258/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1) `REAL300025478931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478931 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 22, 30, 30, 50, 50, 78, 124, 201, 201, 201, 201, 201, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 22, 22, 30, 30, 30, 78, 78, 201, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 559 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478931 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 103, 153, 103, 103, 103, 98, 72, 48, 72, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 103, 103, 103, 103, 103, 98, 98, 72, 72, 72, 26, 26, 1, 103, 103, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 668 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478931 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)ON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 16, 16, 28, 47, 103, 103, 103, 103, 103, 1, 7, 7, 7, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 103, 1, 1, 7] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 252 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478931 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478931 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478931/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478931 Building REAL300025478932 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478932' /scratch/stefan/7787258/working/building/REAL300025478932 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478932 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478932/0 /scratch/stefan/7787258/working/building/REAL300025478932 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/829 `/scratch/stefan/7787258/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(F)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478932 none CN(CC1CCN(C(=O)C2(F)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 1, 15, 32, 32, 63, 84, 122, 122, 122, 122, 122, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 63, 63, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478932 none CN(CC1CCN(C(=O)C2(F)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 52, 75, 108, 122, 122, 122, 122, 165, 165, 201, 201, 201, 201, 201, 201, 122, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 108, 108, 122, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 29, 29, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 807 number of broken/clashed sets: 80 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478932 none CN(CC1CCN(C(=O)C2(F)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 32, 63, 63, 117, 150, 201, 201, 201, 201, 201, 32, 32, 32, 13, 13, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 117, 117, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51]) total number of confs: 615 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478932 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478932 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478932/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478932 Building REAL300025478933 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478933' /scratch/stefan/7787258/working/building/REAL300025478933 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478933 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478933/0 /scratch/stefan/7787258/working/building/REAL300025478933 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/830 `/scratch/stefan/7787258/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478933 none CC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 14, 14, 6, 2, 1, 2, 1, 1, 1, 1, 1, 3, 4, 4, 6, 6, 14, 24, 100, 100, 100, 100, 100, 1, 17, 17, 17, 17, 17, 14, 14, 14, 10, 10, 6, 6, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 14, 14, 100, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 52, 53, 41, 7, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 239 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478933 none CC[N@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 201, 201, 153, 100, 100, 100, 100, 100, 100, 68, 58, 51, 58, 34, 51, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 153, 153, 100, 100, 100, 100, 100, 68, 68, 58, 58, 58, 34, 34, 1, 100, 100] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 953 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478933 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478933/1 /scratch/stefan/7787258/working/building/REAL300025478933 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/831 `/scratch/stefan/7787258/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478933.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING: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: REAL300025478933 none CC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 13, 10, 13, 13, 6, 2, 1, 2, 1, 1, 1, 1, 1, 3, 4, 4, 6, 6, 14, 24, 93, 93, 93, 93, 93, 1, 14, 14, 14, 14, 14, 13, 13, 13, 10, 10, 6, 6, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 14, 14, 93, 1, 1] 172 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 52, 53, 41, 7, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 215 number of broken/clashed sets: 171 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478933 none CC[N@@H+](C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [172, 172, 166, 172, 172, 145, 93, 93, 93, 93, 93, 93, 63, 57, 53, 57, 32, 53, 13, 1, 1, 1, 1, 1, 1, 1, 93, 172, 172, 172, 172, 172, 172, 172, 172, 166, 166, 145, 145, 93, 93, 93, 93, 93, 63, 63, 57, 57, 57, 32, 32, 1, 93, 93] 172 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 785 number of broken/clashed sets: 171 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478933 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478933 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478933/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478933/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478933 Building REAL300025478934 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478934' /scratch/stefan/7787258/working/building/REAL300025478934 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478934 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478934/0 /scratch/stefan/7787258/working/building/REAL300025478934 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/832 `/scratch/stefan/7787258/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC23CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478934 none CN(CC1CCN(C(=O)C2CC23CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 1, 13, 30, 30, 63, 84, 145, 145, 145, 145, 145, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 63, 63, 145] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 404 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478934 none CN(CC1CCN(C(=O)C2CC23CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 64, 78, 122, 145, 145, 145, 145, 165, 165, 201, 201, 201, 201, 201, 201, 145, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 122, 122, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 37, 37, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 818 number of broken/clashed sets: 88 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478934 none CN(CC1CCN(C(=O)C2CC23CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 32, 59, 59, 107, 139, 201, 201, 201, 201, 201, 32, 32, 32, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 597 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478934 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478934 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478934/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478934 Building REAL300025478935 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478935' /scratch/stefan/7787258/working/building/REAL300025478935 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478935 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478935/0 /scratch/stefan/7787258/working/building/REAL300025478935 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/833 `/scratch/stefan/7787258/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478935 none CC1=CON=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 19, 29, 29, 49, 49, 75, 123, 201, 201, 201, 201, 201, 7, 2, 2, 2, 1, 7, 7, 7, 7, 7, 19, 19, 29, 29, 29, 75, 75, 201, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 533 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: REAL300025478935 none CC1=CON=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 149, 191, 149, 149, 149, 131, 94, 59, 94, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 149, 149, 149, 149, 149, 131, 131, 94, 94, 94, 29, 29, 1, 149, 149] 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, 43, 44]) total number of confs: 743 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: REAL300025478935 none CC1=CON=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 25, 25, 42, 72, 149, 149, 149, 149, 149, 1, 8, 8, 8, 7, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 42, 42, 149, 1, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478935 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478935 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478935/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478935 Building REAL300025478936 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478936' /scratch/stefan/7787258/working/building/REAL300025478936 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478936 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478936/0 /scratch/stefan/7787258/working/building/REAL300025478936 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/834 `/scratch/stefan/7787258/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025478936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478936 none CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 23, 37, 128, 128, 128, 128, 128, 1, 11, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 128, 1, 1, 19, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52]) total number of confs: 302 number of broken/clashed sets: 122 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478936 none CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 12, 12, 19, 19, 19, 19, 31, 35, 35, 40, 40, 74, 109, 201, 201, 201, 201, 201, 19, 1, 1, 1, 7, 7, 7, 7, 7, 5, 19, 19, 19, 19, 19, 31, 31, 35, 35, 35, 74, 74, 201, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 543 number of broken/clashed sets: 122 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478936 none CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 143, 128, 143, 128, 128, 128, 114, 73, 53, 73, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 128, 193, 201, 201, 193, 193, 193, 193, 193, 193, 128, 128, 128, 128, 128, 114, 114, 73, 73, 73, 30, 30, 1, 128, 128, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 885 number of broken/clashed sets: 122 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478936 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478936 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478936/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478936 Building REAL300025478937 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478937' /scratch/stefan/7787258/working/building/REAL300025478937 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478937 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478937/0 /scratch/stefan/7787258/working/building/REAL300025478937 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/835 `/scratch/stefan/7787258/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2N=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478937 none CN(CC1CCN(C(=O)CN2N=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 19, 57, 57, 57, 57, 1, 10, 15, 15, 22, 24, 53, 53, 53, 53, 53, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 19, 19, 57, 1, 1, 22, 22, 53] 197 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 244 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478937 none CN(CC1CCN(C(=O)CN2N=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [42, 40, 42, 46, 53, 53, 53, 53, 65, 65, 130, 197, 197, 197, 197, 53, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 46, 46, 53, 53, 53, 53, 53, 130, 130, 197, 53, 53, 29, 29, 1] 197 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 670 number of broken/clashed sets: 107 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478937 none CN(CC1CCN(C(=O)CN2N=CN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [116, 88, 58, 57, 57, 57, 37, 8, 37, 1, 1, 1, 1, 1, 1, 57, 116, 138, 138, 160, 162, 197, 197, 197, 197, 197, 116, 116, 116, 88, 88, 57, 57, 57, 57, 57, 8, 8, 1, 57, 57, 160, 160, 197] 197 rigid atoms, others: [38, 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, 39, 40, 41, 42, 43]) total number of confs: 649 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478937 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478937 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478937/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478937 Building REAL300025478938 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478938' /scratch/stefan/7787258/working/building/REAL300025478938 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478938 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478938/0 /scratch/stefan/7787258/working/building/REAL300025478938 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/836 `/scratch/stefan/7787258/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478938 none CCCC[C@@H](C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 25, 42, 85, 85, 85, 85, 85, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 25, 25, 85, 1, 1] 201 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 52, 53, 41, 7, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478938 none CCCC[C@@H](C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 90, 163, 163, 85, 90, 85, 85, 85, 72, 57, 39, 57, 22, 39, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 85, 85, 85, 85, 85, 72, 72, 57, 57, 57, 22, 22, 1, 85, 85] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 927 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478938 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478938 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478938/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478938 Building REAL300025478939 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478939' /scratch/stefan/7787258/working/building/REAL300025478939 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478939 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478939/0 /scratch/stefan/7787258/working/building/REAL300025478939 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/837 `/scratch/stefan/7787258/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478939 none C=CCC(CC=C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 7, 3, 7, 14, 23, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 16, 16, 22, 29, 66, 66, 66, 66, 66, 1, 27, 27, 27, 15, 15, 7, 14, 14, 23, 23, 23, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 22, 22, 66, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 332 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478939 none C=CCC(CC=C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 173, 143, 79, 143, 174, 196, 66, 79, 66, 66, 66, 54, 46, 36, 46, 17, 36, 13, 1, 1, 1, 1, 1, 1, 1, 66, 196, 196, 196, 173, 173, 143, 174, 174, 196, 196, 196, 66, 66, 66, 66, 66, 54, 54, 46, 46, 46, 17, 17, 1, 66, 66] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 1111 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478939 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478939 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478939/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478939 Building REAL300025478940 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478940' /scratch/stefan/7787258/working/building/REAL300025478940 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478940 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478940/0 /scratch/stefan/7787258/working/building/REAL300025478940 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/838 `/scratch/stefan/7787258/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478940 none CN(CC1CCN(C(=O)C2(C)CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 13, 30, 30, 64, 87, 151, 151, 151, 151, 151, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 64, 64, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 405 number of broken/clashed sets: 146 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478940 none CN(CC1CCN(C(=O)C2(C)CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 75, 99, 140, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 151, 34, 75, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 140, 140, 151, 151, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 151, 34, 34, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 816 number of broken/clashed sets: 146 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478940 none CN(CC1CCN(C(=O)C2(C)CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 22, 49, 49, 101, 135, 201, 201, 201, 201, 201, 22, 22, 22, 9, 9, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 101, 101, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52]) total number of confs: 589 number of broken/clashed sets: 146 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478940 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478940 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478940/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478940 Building REAL300025478941 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478941' /scratch/stefan/7787258/working/building/REAL300025478941 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478941 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478941/0 /scratch/stefan/7787258/working/building/REAL300025478941 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/839 `/scratch/stefan/7787258/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478941 none CCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 28, 48, 101, 101, 101, 101, 101, 1, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 101, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 286 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478941 none CCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 201, 201, 108, 101, 108, 101, 101, 101, 90, 72, 48, 72, 25, 48, 13, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 101, 101, 101, 101, 101, 90, 90, 72, 72, 72, 25, 25, 1, 101, 101] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 923 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478941 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478941 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478941/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478941 Building REAL300025478942 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478942' /scratch/stefan/7787258/working/building/REAL300025478942 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478942 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478942/0 /scratch/stefan/7787258/working/building/REAL300025478942 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/840 `/scratch/stefan/7787258/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478942 none CC(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 4, 6, 6, 1, 4, 1, 1, 1, 1, 1, 4, 6, 6, 8, 8, 19, 31, 77, 77, 77, 77, 77, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 77, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478942 none CC(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 201, 201, 77, 118, 77, 77, 77, 65, 40, 36, 40, 23, 36, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 77, 77, 65, 65, 40, 40, 40, 23, 23, 1, 77, 77] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 964 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478942 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478942 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478942/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478942 Building REAL300025478943 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478943' /scratch/stefan/7787258/working/building/REAL300025478943 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478943 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478943/0 /scratch/stefan/7787258/working/building/REAL300025478943 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/841 `/scratch/stefan/7787258/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478943 none C=CC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 5, 13, 13, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 25, 40, 110, 110, 110, 110, 110, 1, 19, 19, 19, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 110, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 310 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478943 none C=CC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 172, 201, 201, 113, 110, 113, 110, 110, 110, 94, 63, 46, 63, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 172, 110, 110, 110, 110, 110, 94, 94, 63, 63, 63, 28, 28, 1, 110, 110] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 943 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478943 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478943 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478943/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478943 Building REAL300025478944 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478944' /scratch/stefan/7787258/working/building/REAL300025478944 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478944 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478944/0 /scratch/stefan/7787258/working/building/REAL300025478944 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/842 `/scratch/stefan/7787258/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2N=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478944 none CN(CC1CCN(C(=O)CN2N=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 18, 29, 29, 29, 29, 1, 9, 14, 14, 23, 23, 48, 48, 48, 48, 48, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 29, 29, 1, 1, 23, 23, 48] 112 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478944 none CN(CC1CCN(C(=O)CN2N=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [38, 36, 38, 44, 48, 48, 48, 48, 64, 64, 112, 112, 112, 112, 112, 48, 28, 36, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 44, 44, 48, 48, 48, 48, 48, 112, 112, 112, 112, 48, 48, 28, 28, 1] 112 rigid atoms, others: [44, 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]) total number of confs: 469 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478944 none CN(CC1CCN(C(=O)CN2N=CC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [61, 48, 35, 35, 35, 35, 22, 7, 22, 1, 1, 1, 1, 1, 1, 35, 61, 75, 75, 85, 85, 112, 112, 112, 112, 112, 61, 61, 61, 48, 48, 35, 35, 35, 35, 35, 7, 7, 1, 1, 35, 35, 85, 85, 112] 112 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 350 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478944 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478944 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478944/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478944 Building REAL300025478945 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478945' /scratch/stefan/7787258/working/building/REAL300025478945 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478945 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478945/0 /scratch/stefan/7787258/working/building/REAL300025478945 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/843 `/scratch/stefan/7787258/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478945 none CC1CCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 17, 33, 33, 56, 56, 91, 135, 201, 201, 201, 201, 201, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 33, 33, 33, 91, 91, 201, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 39, 36, 38, 5, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 570 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478945 none CC1CCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 185, 201, 185, 185, 185, 155, 96, 66, 96, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 185, 185, 155, 155, 96, 96, 96, 28, 28, 1, 185, 185] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 755 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478945 none CC1CCCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 28, 28, 56, 90, 185, 185, 185, 185, 185, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 56, 56, 185, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 443 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478945 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478945 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478945/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478945 Building REAL300025478946 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478946' /scratch/stefan/7787258/working/building/REAL300025478946 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478946 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478946/0 /scratch/stefan/7787258/working/building/REAL300025478946 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/844 `/scratch/stefan/7787258/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025478946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478946 none CC1CCCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 20, 30, 30, 50, 50, 78, 116, 201, 201, 201, 201, 201, 7, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 30, 30, 30, 78, 78, 201, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 36, 26, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 546 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: REAL300025478946 none CC1CCCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 136, 122, 136, 122, 122, 122, 107, 75, 54, 75, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 107, 107, 75, 75, 75, 25, 25, 1, 122, 122, 201, 201] 201 rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 785 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: REAL300025478946 none CC1CCCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 40, 61, 122, 122, 122, 122, 122, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 40, 40, 122, 1, 1, 7, 7] 201 rigid atoms, others: [6, 38, 39, 8, 9, 10, 11, 12, 40, 51, 52, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 319 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478946 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478946 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478946/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478946 Building REAL300025478947 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478947' /scratch/stefan/7787258/working/building/REAL300025478947 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478947 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478947/0 /scratch/stefan/7787258/working/building/REAL300025478947 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/845 `/scratch/stefan/7787258/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478947 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 25, 38, 38, 56, 56, 81, 122, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 25, 25, 38, 38, 38, 81, 81, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 562 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: REAL300025478947 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 158, 138, 158, 138, 138, 138, 118, 87, 64, 87, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 118, 118, 87, 87, 87, 29, 29, 1, 138, 138] 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, 46, 47]) total number of confs: 677 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: REAL300025478947 none CC1=NC=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 23, 23, 42, 63, 138, 138, 138, 138, 138, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 42, 42, 138, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478947 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478947 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478947/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478947 Building REAL300025478948 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478948' /scratch/stefan/7787258/working/building/REAL300025478948 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478948 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478948/0 /scratch/stefan/7787258/working/building/REAL300025478948 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/846 `/scratch/stefan/7787258/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478948 none C=CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 16, 11, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 19, 29, 83, 83, 83, 83, 83, 1, 27, 27, 27, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 19, 19, 83, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478948 none C=CCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 83, 83, 83, 83, 83, 83, 64, 35, 32, 35, 23, 32, 12, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 179, 179, 83, 83, 83, 83, 83, 64, 64, 35, 35, 35, 23, 23, 1, 83, 83] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 853 number of broken/clashed sets: 153 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478948 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478948 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478948/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478948 Building REAL300025478949 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478949' /scratch/stefan/7787258/working/building/REAL300025478949 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478949 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478949/0 /scratch/stefan/7787258/working/building/REAL300025478949 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/847 `/scratch/stefan/7787258/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478949 none CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 15, 15, 28, 47, 82, 82, 82, 82, 82, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 82, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478949 none CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 201, 201, 82, 123, 82, 82, 82, 81, 63, 44, 63, 23, 44, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 82, 82, 81, 81, 63, 63, 63, 23, 23, 1, 82, 82] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 925 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478949 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478949 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478949/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478949 Building REAL300025478950 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478950' /scratch/stefan/7787258/working/building/REAL300025478950 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478950 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478950/0 /scratch/stefan/7787258/working/building/REAL300025478950 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/848 `/scratch/stefan/7787258/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478950 none CCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 1, 4, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 25, 38, 105, 105, 105, 105, 105, 1, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 105, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 258 number of broken/clashed sets: 171 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478950 none CCCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 145, 188, 188, 105, 145, 105, 105, 105, 81, 49, 44, 49, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 188, 188, 105, 105, 105, 105, 105, 81, 81, 49, 49, 49, 28, 28, 1, 105, 105] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 896 number of broken/clashed sets: 171 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478950 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478950 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478950/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478950 Building REAL300025478951 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478951' /scratch/stefan/7787258/working/building/REAL300025478951 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478951 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478951/0 /scratch/stefan/7787258/working/building/REAL300025478951 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/849 `/scratch/stefan/7787258/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478951 none CN(CC1CCN(C(=O)C2(C(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 6, 6, 8, 11, 11, 8, 8, 1, 6, 9, 9, 13, 13, 18, 18, 18, 18, 18, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 11, 11, 8, 8, 8, 8, 1, 1, 13, 13, 18] 29 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 95 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: REAL300025478951 none CN(CC1CCN(C(=O)C2(C(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 18, 18, 18, 18, 18, 26, 26, 29, 29, 29, 29, 29, 18, 14, 17, 12, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 18, 18, 14, 14, 1] 29 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 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: REAL300025478951 none CN(CC1CCN(C(=O)C2(C(N)=O)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 8, 8, 8, 8, 3, 1, 3, 1, 1, 6, 6, 1, 1, 8, 16, 20, 20, 25, 25, 29, 29, 29, 29, 29, 16, 16, 16, 12, 12, 8, 8, 8, 8, 8, 6, 6, 1, 1, 1, 1, 8, 8, 25, 25, 29] 29 rigid atoms, others: [38, 7, 40, 9, 10, 39, 13, 14, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478951 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478951 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478951/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478951 Building REAL300025478952 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478952' /scratch/stefan/7787258/working/building/REAL300025478952 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478952 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478952/0 /scratch/stefan/7787258/working/building/REAL300025478952 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/850 `/scratch/stefan/7787258/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478952 none CN(CC1CCN(C(=O)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 11, 1, 13, 32, 32, 57, 82, 139, 139, 139, 139, 139, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 11, 1, 1, 57, 57, 139] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 12, 35, 36, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 37, 38, 39]) total number of confs: 389 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478952 none CN(CC1CCN(C(=O)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 69, 88, 129, 139, 139, 139, 139, 187, 187, 201, 201, 139, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 129, 129, 139, 139, 139, 139, 139, 201, 201, 139, 139, 31, 31, 1] 201 rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 802 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478952 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478952 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478952/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478952 Building REAL300025478953 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478953' /scratch/stefan/7787258/working/building/REAL300025478953 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478953 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478953/0 /scratch/stefan/7787258/working/building/REAL300025478953 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/851 `/scratch/stefan/7787258/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478953 none CC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 28, 38, 38, 54, 54, 81, 118, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 11, 11, 11, 11, 11, 28, 28, 38, 38, 38, 81, 81, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 564 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: REAL300025478953 none CC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 146, 99, 146, 99, 99, 99, 92, 64, 51, 64, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 99, 99, 99, 99, 99, 92, 92, 64, 64, 64, 29, 29, 1, 99, 99] 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, 43, 44]) total number of confs: 676 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: REAL300025478953 none CC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 30, 44, 99, 99, 99, 99, 99, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 99, 1, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 242 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478953 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478953 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478953/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478953 Building REAL300025478954 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478954' /scratch/stefan/7787258/working/building/REAL300025478954 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478954 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478954/0 /scratch/stefan/7787258/working/building/REAL300025478954 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/852 `/scratch/stefan/7787258/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478954 none CN(CC1CCN(C(=O)C2(C)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 1, 11, 25, 25, 48, 61, 98, 98, 98, 98, 98, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 48, 48, 98] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 290 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478954 none CN(CC1CCN(C(=O)C2(C)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 55, 69, 87, 98, 98, 98, 98, 129, 129, 201, 201, 201, 201, 201, 201, 98, 31, 55, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 87, 87, 98, 98, 98, 98, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 98, 31, 31, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 800 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478954 none CN(CC1CCN(C(=O)C2(C)CCCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 14, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 29, 69, 69, 111, 145, 201, 201, 201, 201, 201, 29, 29, 29, 14, 14, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 111, 111, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 50, 51, 52, 53, 54]) total number of confs: 621 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478954 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478954 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478954/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478954 Building REAL300025478955 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478955' /scratch/stefan/7787258/working/building/REAL300025478955 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478955 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478955/0 /scratch/stefan/7787258/working/building/REAL300025478955 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/853 `/scratch/stefan/7787258/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478955 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 6, 12, 12, 16, 19, 27, 27, 27, 27, 27, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 16, 16, 27] 28 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 92 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478955 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 27, 19, 24, 12, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 19, 19, 1] 28 rigid atoms, others: [54, 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, 19, 20, 28, 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: 82 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478955 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 18, 18, 24, 24, 28, 28, 28, 28, 28, 13, 13, 13, 8, 8, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 24, 24, 28] 28 rigid atoms, others: [48, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 49, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478955 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478955 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478955/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478955 Building REAL300025478956 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478956' /scratch/stefan/7787258/working/building/REAL300025478956 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478956 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478956/0 /scratch/stefan/7787258/working/building/REAL300025478956 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/854 `/scratch/stefan/7787258/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478956 none CN(CC1CCN(C(=O)C2(C)CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 1, 14, 37, 37, 89, 117, 183, 183, 183, 183, 183, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 89, 89, 183] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 518 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: REAL300025478956 none CN(CC1CCN(C(=O)C2(C)CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 80, 109, 159, 183, 183, 183, 183, 196, 196, 201, 201, 201, 201, 201, 183, 42, 80, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 159, 159, 183, 183, 183, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 42, 42, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 816 number of broken/clashed sets: 98 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478956 none CN(CC1CCN(C(=O)C2(C)CC=CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 24, 54, 54, 106, 136, 201, 201, 201, 201, 201, 24, 24, 24, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 106, 106, 201] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 45, 46, 47, 48, 49]) total number of confs: 580 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478956 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478956 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478956/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478956 Building REAL300025478957 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478957' /scratch/stefan/7787258/working/building/REAL300025478957 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478957 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478957/0 /scratch/stefan/7787258/working/building/REAL300025478957 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/855 `/scratch/stefan/7787258/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478957 none CN(CC1CCN(C(=O)C2=CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 1, 12, 24, 24, 45, 61, 109, 109, 109, 109, 109, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 45, 45, 109] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 300 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478957 none CN(CC1CCN(C(=O)C2=CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 64, 67, 102, 109, 109, 109, 109, 122, 122, 201, 201, 201, 201, 201, 201, 109, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 102, 102, 109, 109, 109, 109, 109, 201, 201, 201, 201, 201, 109, 109, 37, 37, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 634 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478957 none CN(CC1CCN(C(=O)C2=CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 32, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 13, 51, 75, 75, 114, 141, 201, 201, 201, 201, 201, 51, 51, 51, 32, 32, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 13, 13, 114, 114, 201] 201 rigid atoms, others: [37, 7, 9, 10, 11, 12, 13, 14, 15, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 613 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478957 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478957 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478957/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478957 Building REAL300025478958 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478958' /scratch/stefan/7787258/working/building/REAL300025478958 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478958 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478958/0 /scratch/stefan/7787258/working/building/REAL300025478958 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/856 `/scratch/stefan/7787258/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025478958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478958 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 12, 12, 28, 48, 179, 179, 179, 179, 179, 1, 6, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 28, 28, 179, 1, 1, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 361 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478958 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 201, 179, 179, 179, 148, 89, 62, 89, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 179, 148, 148, 89, 89, 89, 31, 31, 1, 179, 179, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 804 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478958 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478958 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478958/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478958 Building REAL300025478959 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478959' /scratch/stefan/7787258/working/building/REAL300025478959 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478959 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478959/0 /scratch/stefan/7787258/working/building/REAL300025478959 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/857 `/scratch/stefan/7787258/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478959 none CC1CC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 15, 15, 23, 23, 23, 23, 39, 51, 51, 52, 52, 89, 117, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 39, 39, 51, 51, 51, 89, 89, 201, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 4, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 592 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478959 none CC1CC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 97, 97, 97, 97, 97, 97, 82, 53, 41, 53, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 201, 201, 197, 197, 97, 97, 97, 97, 97, 82, 82, 53, 53, 53, 28, 28, 1, 97, 97] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 846 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478959 none CC1CC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 21, 33, 97, 97, 97, 97, 97, 1, 23, 23, 23, 23, 23, 23, 23, 12, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 21, 21, 97, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 283 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478959 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478959 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478959/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478959 Building REAL300025478960 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478960' /scratch/stefan/7787258/working/building/REAL300025478960 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478960 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478960/0 /scratch/stefan/7787258/working/building/REAL300025478960 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/858 `/scratch/stefan/7787258/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478960 none CCCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 3, 1, 1, 1, 2, 2, 3, 3, 3, 3, 7, 12, 12, 26, 26, 51, 89, 175, 175, 175, 175, 175, 3, 1, 1, 6, 6, 6, 6, 6, 4, 4, 3, 3, 3, 3, 3, 3, 3, 7, 7, 12, 12, 12, 51, 51, 175, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 435 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: REAL300025478960 none CCCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 175, 175, 172, 175, 172, 172, 172, 141, 100, 60, 100, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 172, 175, 175, 201, 201, 201, 201, 201, 201, 201, 175, 175, 172, 172, 172, 172, 172, 141, 141, 100, 100, 100, 28, 28, 1, 172, 172, 175, 175, 175, 175] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 807 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: REAL300025478960 none CCCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 25, 25, 50, 87, 172, 172, 172, 172, 172, 1, 3, 3, 7, 7, 7, 7, 7, 5, 5, 4, 4, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 50, 50, 172, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 431 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478960 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478960 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478960/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478960 Building REAL300025478961 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478961' /scratch/stefan/7787258/working/building/REAL300025478961 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478961 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478961/0 /scratch/stefan/7787258/working/building/REAL300025478961 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/859 `/scratch/stefan/7787258/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478961 none C=C1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 18, 28, 28, 49, 49, 79, 119, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 28, 28, 28, 79, 79, 201, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 33, 49, 50, 51, 52, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 545 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478961 none C=C1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 136, 122, 136, 122, 122, 122, 107, 78, 56, 78, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 107, 107, 78, 78, 78, 26, 26, 1, 122, 122, 201, 201, 201, 201] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 778 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478961 none C=C1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 39, 63, 122, 122, 122, 122, 122, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 39, 39, 122, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 319 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478961 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478961 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478961/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478961 Building REAL300025478962 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478962' /scratch/stefan/7787258/working/building/REAL300025478962 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478962 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478962/0 /scratch/stefan/7787258/working/building/REAL300025478962 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/860 `/scratch/stefan/7787258/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478962 none C=CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 5, 1, 1, 1, 3, 3, 5, 5, 5, 5, 13, 21, 21, 37, 37, 51, 69, 132, 132, 132, 132, 132, 5, 1, 1, 15, 15, 15, 7, 7, 5, 5, 5, 5, 5, 5, 5, 13, 13, 21, 21, 21, 51, 51, 132, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 385 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: REAL300025478962 none C=CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 132, 126, 100, 126, 100, 100, 100, 82, 54, 34, 54, 17, 34, 13, 1, 1, 1, 1, 1, 1, 1, 100, 132, 132, 201, 201, 201, 201, 201, 143, 143, 100, 100, 100, 100, 100, 82, 82, 54, 54, 54, 17, 17, 1, 100, 100, 132, 132, 132, 132] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 900 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: REAL300025478962 none C=CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 8, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 12, 12, 23, 23, 34, 47, 100, 100, 100, 100, 100, 1, 5, 5, 19, 19, 19, 10, 10, 8, 8, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 34, 34, 100, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 310 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478962 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478962 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478962/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478962 Building REAL300025478963 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478963' /scratch/stefan/7787258/working/building/REAL300025478963 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478963 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478963/0 /scratch/stefan/7787258/working/building/REAL300025478963 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/861 `/scratch/stefan/7787258/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478963 none C=CC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 6, 6, 6, 9, 1, 6, 1, 1, 1, 1, 1, 6, 10, 10, 21, 21, 47, 78, 170, 170, 170, 170, 170, 1, 8, 8, 8, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 47, 47, 170, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 429 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478963 none C=CC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 199, 199, 201, 170, 199, 170, 170, 170, 152, 100, 68, 100, 28, 68, 13, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 199, 199, 199, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 152, 152, 100, 100, 100, 28, 28, 1, 170, 170] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 791 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478963 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478963 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478963/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478963 Building REAL300025478964 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478964' /scratch/stefan/7787258/working/building/REAL300025478964 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478964 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478964/0 /scratch/stefan/7787258/working/building/REAL300025478964 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/862 `/scratch/stefan/7787258/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC(F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478964 none CN(CC1CCN(C(=O)C2CCC(F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 1, 14, 33, 33, 59, 81, 138, 138, 138, 138, 138, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 59, 59, 138] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 369 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478964 none CN(CC1CCN(C(=O)C2CCC(F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 76, 92, 120, 138, 138, 138, 138, 141, 141, 201, 201, 201, 201, 201, 201, 138, 38, 76, 13, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 120, 120, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 38, 38, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 804 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478964 none CN(CC1CCN(C(=O)C2CCC(F)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 31, 64, 64, 101, 138, 201, 201, 201, 201, 201, 31, 31, 31, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 101, 101, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51]) total number of confs: 569 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478964 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478964 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478964/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478964 Building REAL300025478965 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478965' /scratch/stefan/7787258/working/building/REAL300025478965 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478965 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478965/0 /scratch/stefan/7787258/working/building/REAL300025478965 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/863 `/scratch/stefan/7787258/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C[C@H]2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478965 none CN(CC1CCN(C(=O)C[C@H]2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 15, 27, 27, 27, 27, 27, 1, 8, 12, 12, 16, 16, 37, 37, 37, 37, 37, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 27, 27, 27, 27, 27, 27, 1, 1, 16, 16, 37] 92 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478965 none CN(CC1CCN(C(=O)C[C@H]2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [30, 28, 30, 33, 37, 37, 37, 37, 43, 43, 84, 92, 92, 92, 92, 92, 37, 23, 28, 13, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 33, 33, 37, 37, 37, 37, 37, 84, 84, 92, 92, 92, 92, 92, 92, 37, 37, 23, 23, 1] 92 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 372 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478965 none CN(CC1CCN(C(=O)C[C@H]2CCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [58, 47, 27, 27, 27, 27, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 27, 58, 66, 66, 73, 73, 92, 92, 92, 92, 92, 58, 58, 58, 47, 47, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 27, 27, 73, 73, 92] 92 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 327 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478965 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478965 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478965/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478965 Building REAL300025478966 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478966' /scratch/stefan/7787258/working/building/REAL300025478966 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478966 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478966/0 /scratch/stefan/7787258/working/building/REAL300025478966 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/864 `/scratch/stefan/7787258/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025478966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478966 none C=CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 10, 10, 20, 20, 49, 80, 201, 201, 201, 201, 201, 2, 1, 1, 1, 6, 6, 6, 3, 3, 2, 2, 2, 2, 2, 6, 6, 10, 10, 10, 49, 49, 201, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478966 none C=CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 120, 80, 120, 29, 80, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 120, 120, 120, 29, 29, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 745 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: REAL300025478966 none C=CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 20, 20, 49, 80, 201, 201, 201, 201, 201, 1, 2, 2, 2, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 49, 49, 201, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 448 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478966 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478966 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478966/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478966 Building REAL300025478967 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478967' /scratch/stefan/7787258/working/building/REAL300025478967 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478967 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478967/0 /scratch/stefan/7787258/working/building/REAL300025478967 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/865 `/scratch/stefan/7787258/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478967 none CN(CC1CCN(C(=O)CC2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 23, 23, 23, 23, 23, 1, 8, 10, 10, 12, 12, 28, 28, 28, 28, 28, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 23, 23, 23, 23, 23, 23, 23, 1, 1, 12, 12, 28] 68 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 130 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: REAL300025478967 none CN(CC1CCN(C(=O)CC2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 25, 28, 28, 28, 28, 31, 31, 68, 68, 68, 68, 68, 68, 28, 21, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 25, 25, 28, 28, 28, 28, 28, 68, 68, 68, 68, 68, 68, 68, 68, 68, 28, 28, 21, 21, 1] 68 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 265 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: REAL300025478967 none CN(CC1CCN(C(=O)CC2=CCOCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 34, 23, 23, 23, 23, 15, 6, 15, 1, 1, 1, 1, 1, 1, 1, 23, 42, 48, 48, 53, 53, 68, 68, 68, 68, 68, 42, 42, 42, 34, 34, 23, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 23, 23, 53, 53, 68] 68 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 48, 49, 50]) total number of confs: 222 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478967 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478967 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478967/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478967 Building REAL300025478968 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478968' /scratch/stefan/7787258/working/building/REAL300025478968 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478968 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478968/0 /scratch/stefan/7787258/working/building/REAL300025478968 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/866 `/scratch/stefan/7787258/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1) `REAL300025478968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478968 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 17, 24, 24, 27, 27, 52, 79, 129, 129, 129, 129, 129, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 6, 6, 6, 17, 17, 24, 24, 24, 52, 52, 129, 5, 5, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 48, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 372 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478968 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 129, 114, 87, 114, 87, 87, 87, 76, 55, 43, 55, 25, 43, 13, 1, 1, 1, 1, 1, 1, 1, 87, 129, 129, 129, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 76, 76, 55, 55, 55, 25, 25, 1, 87, 87, 129, 129] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 904 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478968 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 26, 37, 87, 87, 87, 87, 87, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 26, 26, 87, 1, 1, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 241 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478968 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478968 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478968/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478968 Building REAL300025478969 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478969' /scratch/stefan/7787258/working/building/REAL300025478969 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478969 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478969/0 /scratch/stefan/7787258/working/building/REAL300025478969 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/867 `/scratch/stefan/7787258/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478969 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 3, 3, 6, 6, 6, 6, 14, 20, 20, 42, 42, 69, 114, 201, 201, 201, 201, 201, 6, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 14, 14, 20, 20, 20, 69, 69, 201, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 45, 46, 47, 48, 23, 24] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 501 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: REAL300025478969 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 180, 201, 180, 180, 180, 166, 116, 70, 116, 29, 70, 13, 1, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 166, 166, 116, 116, 116, 29, 29, 1, 180, 180, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 751 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: REAL300025478969 none CCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 12, 12, 34, 34, 61, 99, 180, 180, 180, 180, 180, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 61, 61, 180, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 441 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478969 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478969 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478969/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478969 Building REAL300025478970 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478970' /scratch/stefan/7787258/working/building/REAL300025478970 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478970 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478970/0 /scratch/stefan/7787258/working/building/REAL300025478970 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/868 `/scratch/stefan/7787258/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025478970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478970 none CC(C)[C@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 5, 6, 1, 5, 1, 1, 1, 1, 1, 4, 7, 7, 10, 10, 23, 37, 91, 91, 91, 91, 91, 1, 6, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 23, 23, 91, 1, 1, 8, 8, 8, 8, 8, 8] 116 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 231 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478970 none CC(C)[C@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 105, 116, 104, 105, 91, 104, 91, 91, 91, 81, 77, 62, 77, 32, 62, 13, 1, 1, 1, 1, 1, 1, 1, 91, 105, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 91, 91, 91, 91, 91, 81, 81, 77, 77, 77, 32, 32, 1, 91, 91, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 513 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478970 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478970 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478970/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478970 Building REAL300025478971 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478971' /scratch/stefan/7787258/working/building/REAL300025478971 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478971 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478971/0 /scratch/stefan/7787258/working/building/REAL300025478971 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/869 `/scratch/stefan/7787258/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478971 none CCC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 16, 25, 25, 44, 44, 73, 116, 201, 201, 201, 201, 201, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 25, 25, 25, 73, 73, 201, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 38, 39, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 520 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478971 none CCC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 182, 200, 182, 182, 182, 160, 104, 66, 104, 28, 66, 13, 1, 1, 1, 1, 1, 1, 1, 182, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 160, 160, 104, 104, 104, 28, 28, 1, 182, 182] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 767 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478971 none CCC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 26, 26, 54, 89, 182, 182, 182, 182, 182, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 54, 54, 182, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 440 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478971 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478971 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478971/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478971 Building REAL300025478972 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478972' /scratch/stefan/7787258/working/building/REAL300025478972 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478972 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478972/0 /scratch/stefan/7787258/working/building/REAL300025478972 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/870 `/scratch/stefan/7787258/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478972 none CN(CC1CCN(C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 12, 30, 30, 66, 89, 145, 145, 145, 145, 145, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 66, 66, 145] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 403 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478972 none CN(CC1CCN(C(=O)C(C)(C)C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 95, 134, 145, 145, 145, 145, 201, 201, 201, 201, 201, 145, 32, 71, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 134, 134, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 32, 32, 1] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 814 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478972 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478972 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478972/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478972 Building REAL300025478973 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478973' /scratch/stefan/7787258/working/building/REAL300025478973 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478973 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478973/0 /scratch/stefan/7787258/working/building/REAL300025478973 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/871 `/scratch/stefan/7787258/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1) `REAL300025478973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478973 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 21, 29, 29, 39, 39, 77, 117, 201, 201, 201, 201, 201, 8, 1, 1, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 21, 21, 29, 29, 29, 77, 77, 201, 8, 8, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 48, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 541 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478973 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 184, 201, 184, 184, 184, 150, 96, 59, 96, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 184, 184, 184, 184, 184, 150, 150, 96, 96, 96, 27, 27, 1, 184, 184, 201, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 772 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: REAL300025478973 none CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 25, 25, 54, 88, 184, 184, 184, 184, 184, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 54, 54, 184, 1, 1, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 452 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478973 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478973 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478973/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478973 Building REAL300025478974 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478974' /scratch/stefan/7787258/working/building/REAL300025478974 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478974 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478974/0 /scratch/stefan/7787258/working/building/REAL300025478974 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/872 `/scratch/stefan/7787258/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC23CCOC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478974 none CN(CC1CCN(C(=O)C2CC23CCOC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 1, 14, 33, 33, 65, 85, 149, 149, 149, 149, 149, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 65, 65, 149] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 47, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 412 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: REAL300025478974 none CN(CC1CCN(C(=O)C2CC23CCOC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 66, 83, 125, 149, 149, 149, 149, 188, 188, 201, 201, 201, 201, 201, 201, 149, 33, 66, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 125, 125, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 33, 33, 1] 201 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 815 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: REAL300025478974 none CN(CC1CCN(C(=O)C2CC23CCOC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 35, 64, 64, 119, 148, 201, 201, 201, 201, 201, 35, 35, 35, 18, 18, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 119, 119, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 619 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478974 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478974 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478974/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478974 Building REAL300025478975 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478975' /scratch/stefan/7787258/working/building/REAL300025478975 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478975 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478975/0 /scratch/stefan/7787258/working/building/REAL300025478975 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/873 `/scratch/stefan/7787258/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478975 none COCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 16, 16, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 18, 18, 24, 32, 67, 67, 67, 67, 67, 1, 49, 49, 49, 34, 34, 16, 16, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 24, 24, 67, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 342 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478975 none COCCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 154, 113, 74, 113, 67, 74, 67, 67, 67, 55, 42, 35, 42, 18, 35, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 154, 154, 154, 154, 113, 113, 113, 113, 67, 67, 67, 67, 67, 55, 55, 42, 42, 42, 18, 18, 1, 67, 67] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 949 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478975 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478975 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478975/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478975 Building REAL300025478976 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478976' /scratch/stefan/7787258/working/building/REAL300025478976 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478976 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478976/0 /scratch/stefan/7787258/working/building/REAL300025478976 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/874 `/scratch/stefan/7787258/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478976 none CCC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 6, 6, 6, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 21, 21, 44, 68, 129, 129, 129, 129, 129, 1, 7, 7, 7, 7, 7, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 44, 44, 129, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 362 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478976 none CCC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 201, 201, 201, 201, 129, 144, 129, 129, 129, 117, 82, 55, 82, 25, 55, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 117, 117, 82, 82, 82, 25, 25, 1, 129, 129] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 882 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478976 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478976 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478976/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478976 Building REAL300025478977 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478977' /scratch/stefan/7787258/working/building/REAL300025478977 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478977 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478977/0 /scratch/stefan/7787258/working/building/REAL300025478977 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/875 `/scratch/stefan/7787258/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478977 none CC(C)CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 36, 36, 70, 107, 197, 197, 197, 197, 197, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 70, 70, 197, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 495 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478977 none CC(C)CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 197, 201, 197, 197, 197, 193, 121, 68, 121, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 193, 193, 121, 121, 121, 29, 29, 1, 197, 197] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 775 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478977 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478977 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478977/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478977 Building REAL300025478978 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478978' /scratch/stefan/7787258/working/building/REAL300025478978 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478978 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478978/0 /scratch/stefan/7787258/working/building/REAL300025478978 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/876 `/scratch/stefan/7787258/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478978 none CN(CC1CCN(C(=O)CCCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 14, 21, 21, 37, 79, 79, 1, 8, 12, 12, 15, 15, 38, 38, 38, 38, 38, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 15, 14, 21, 21, 22, 22, 36, 36, 79, 79, 1, 1, 15, 15, 38] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 16, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 386 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478978 none CN(CC1CCN(C(=O)CCCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 32, 33, 38, 38, 38, 38, 48, 48, 124, 135, 135, 170, 201, 201, 38, 27, 31, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 33, 33, 38, 38, 38, 38, 38, 124, 124, 135, 135, 135, 135, 170, 170, 201, 201, 38, 38, 27, 27, 1] 201 rigid atoms, others: [51, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 853 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478978 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478978 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478978/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478978 Building REAL300025478979 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478979' /scratch/stefan/7787258/working/building/REAL300025478979 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478979 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478979/0 /scratch/stefan/7787258/working/building/REAL300025478979 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/877 `/scratch/stefan/7787258/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C2CC2)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025478979 none CN(CC1CCN(C(=O)C(C2CC2)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 7, 7, 1, 6, 8, 8, 9, 9, 18, 18, 18, 18, 18, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 9, 9, 18] 18 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478979 none CN(CC1CCN(C(=O)C(C2CC2)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 1] 18 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 7 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478979 none CN(CC1CCN(C(=O)C(C2CC2)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 7, 7, 7, 7, 5, 2, 5, 1, 2, 4, 4, 1, 1, 1, 7, 10, 13, 13, 14, 14, 18, 18, 18, 18, 18, 10, 10, 10, 8, 8, 7, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 14, 14, 18] 18 rigid atoms, others: [45, 9, 43, 44, 13, 14, 15, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50, 51, 52]) total number of confs: 67 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: REAL300025478979 none CN(CC1CCN(C(=O)C(C2CC2)C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 1, 2, 4, 4, 5, 10, 13, 13, 14, 14, 18, 18, 18, 18, 18, 10, 10, 10, 8, 8, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 14, 14, 18] 18 rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478979 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478979 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478979/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478979 Building REAL300025478980 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478980' /scratch/stefan/7787258/working/building/REAL300025478980 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025478980 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478980/0 /scratch/stefan/7787258/working/building/REAL300025478980 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/878 `/scratch/stefan/7787258/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 20, 45, 45, 45, 45, 1, 10, 15, 15, 23, 25, 54, 54, 54, 54, 54, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 20, 20, 45, 45, 1, 1, 23, 23, 54] 145 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [41, 39, 41, 47, 54, 54, 54, 54, 85, 85, 144, 145, 145, 145, 145, 54, 28, 39, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 47, 47, 54, 54, 54, 54, 54, 144, 144, 145, 145, 54, 54, 28, 28, 1] 145 rigid atoms, others: [44, 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]) total number of confs: 600 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: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [91, 69, 45, 45, 45, 45, 27, 8, 27, 1, 1, 1, 1, 1, 1, 45, 91, 105, 105, 124, 124, 145, 145, 145, 145, 145, 91, 91, 91, 69, 69, 45, 45, 45, 45, 45, 8, 8, 1, 1, 45, 45, 124, 124, 145] 145 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 500 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478980 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025478980/1 /scratch/stefan/7787258/working/building/REAL300025478980 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/879 `/scratch/stefan/7787258/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=NC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478980.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025478980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 45, 45, 45, 45, 1, 10, 15, 15, 25, 27, 57, 57, 57, 57, 57, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 23, 23, 45, 45, 1, 1, 25, 25, 57] 165 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [44, 42, 44, 50, 57, 57, 57, 57, 88, 88, 165, 165, 165, 165, 165, 57, 30, 42, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 50, 50, 57, 57, 57, 57, 57, 165, 165, 165, 165, 57, 57, 30, 30, 1] 165 rigid atoms, others: [44, 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]) total number of confs: 689 number of broken/clashed sets: 87 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478980 none CN(CC1CCN(C(=O)CC2=NC=NN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [93, 67, 45, 45, 45, 45, 26, 7, 26, 1, 1, 1, 1, 1, 1, 45, 93, 113, 113, 134, 134, 165, 165, 165, 165, 165, 93, 93, 93, 67, 67, 45, 45, 45, 45, 45, 7, 7, 1, 1, 45, 45, 134, 134, 165] 165 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 539 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478980 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478980 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025478980/1.* 0: /scratch/stefan/7787258/working/building/REAL300025478980/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478980 Building REAL300025478981 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478981' /scratch/stefan/7787258/working/building/REAL300025478981 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478981 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478981/0 /scratch/stefan/7787258/working/building/REAL300025478981 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/880 `/scratch/stefan/7787258/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1) `REAL300025478981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478981 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 26, 26, 54, 89, 180, 180, 180, 180, 180, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 54, 54, 180, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 442 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: REAL300025478981 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 5, 5, 5, 5, 15, 24, 24, 44, 44, 72, 115, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 15, 15, 24, 24, 24, 72, 72, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 54, 46, 47, 48, 49, 50, 51, 52, 53, 22, 23, 24, 25, 26, 30] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 517 number of broken/clashed sets: 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: REAL300025478981 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 180, 201, 180, 180, 180, 154, 101, 60, 101, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 180, 180, 154, 154, 101, 101, 101, 28, 28, 1, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 768 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478981 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478981 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478981/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478981 Building REAL300025478982 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478982' /scratch/stefan/7787258/working/building/REAL300025478982 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478982 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478982/0 /scratch/stefan/7787258/working/building/REAL300025478982 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/881 `/scratch/stefan/7787258/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025478982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478982 none CCCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 48, 80, 158, 158, 158, 158, 158, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 48, 48, 158, 1, 1, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 39, 48, 49, 23, 36, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 412 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478982 none CCCC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 158, 171, 158, 158, 158, 149, 91, 56, 91, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 158, 149, 149, 91, 91, 91, 26, 26, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 826 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478982 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478982 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478982/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478982 Building REAL300025478983 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478983' /scratch/stefan/7787258/working/building/REAL300025478983 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478983 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478983/0 /scratch/stefan/7787258/working/building/REAL300025478983 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/882 `/scratch/stefan/7787258/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2C=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478983 none CN(CC1CCN(C(=O)C2C=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 1, 16, 38, 38, 76, 100, 163, 163, 163, 163, 163, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 1, 1, 76, 76, 163] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 456 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478983 none CN(CC1CCN(C(=O)C2C=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 76, 99, 138, 163, 163, 163, 163, 176, 176, 201, 201, 201, 201, 201, 201, 163, 41, 76, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 138, 138, 163, 163, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 163, 163, 41, 41, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 806 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478983 none CN(CC1CCN(C(=O)C2C=CC=CC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 16, 7, 6, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 33, 63, 63, 105, 136, 201, 201, 201, 201, 201, 33, 33, 33, 16, 16, 7, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 105, 105, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 569 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478983 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478983 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478983/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478983 Building REAL300025478984 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478984' /scratch/stefan/7787258/working/building/REAL300025478984 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478984 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478984/0 /scratch/stefan/7787258/working/building/REAL300025478984 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/883 `/scratch/stefan/7787258/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478984 none C=C(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 9, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 9, 9, 21, 34, 104, 104, 104, 104, 104, 1, 27, 27, 27, 27, 27, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 21, 21, 104, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 295 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478984 none C=C(C)CCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 125, 104, 125, 104, 104, 104, 83, 47, 41, 47, 29, 41, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 104, 83, 83, 47, 47, 47, 29, 29, 1, 104, 104] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 832 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478984 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478984 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478984/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478984 Building REAL300025478985 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478985' /scratch/stefan/7787258/working/building/REAL300025478985 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478985 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478985/0 /scratch/stefan/7787258/working/building/REAL300025478985 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/884 `/scratch/stefan/7787258/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478985 none CN(CC1CCN(C(=O)C2=CC=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 1, 14, 28, 28, 56, 81, 140, 140, 140, 140, 140, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 56, 56, 140] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 380 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478985 none CN(CC1CCN(C(=O)C2=CC=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 75, 82, 125, 140, 140, 140, 140, 160, 160, 201, 201, 201, 201, 140, 39, 75, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 125, 125, 140, 140, 140, 140, 140, 201, 201, 140, 140, 39, 39, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 722 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478985 none CN(CC1CCN(C(=O)C2=CC=NS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 11, 45, 75, 75, 114, 145, 201, 201, 201, 201, 201, 45, 45, 45, 25, 25, 11, 11, 11, 11, 11, 1, 1, 11, 11, 114, 114, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 611 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478985 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478985 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478985/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478985 Building REAL300025478986 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478986' /scratch/stefan/7787258/working/building/REAL300025478986 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478986 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478986/0 /scratch/stefan/7787258/working/building/REAL300025478986 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/885 `/scratch/stefan/7787258/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478986 none CCC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 17, 26, 26, 37, 37, 61, 98, 201, 201, 201, 201, 201, 8, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 61, 61, 201, 8, 8] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 36, 26, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 493 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478986 none CCC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 162, 191, 162, 162, 162, 145, 98, 65, 98, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 145, 145, 98, 98, 98, 30, 30, 1, 162, 162] 201 rigid atoms, others: [50, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 766 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478986 none CCC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 43, 71, 162, 162, 162, 162, 162, 1, 8, 12, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 43, 43, 162, 1, 1] 201 rigid atoms, others: [6, 38, 39, 8, 9, 10, 11, 12, 40, 51, 52, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 407 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478986 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478986 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478986/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478986 Building REAL300025478987 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478987' /scratch/stefan/7787258/working/building/REAL300025478987 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478987 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478987/0 /scratch/stefan/7787258/working/building/REAL300025478987 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/886 `/scratch/stefan/7787258/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478987 none COCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 10, 10, 25, 25, 52, 87, 168, 168, 168, 168, 168, 2, 1, 1, 10, 10, 10, 4, 4, 3, 3, 2, 2, 2, 2, 2, 5, 5, 10, 10, 10, 52, 52, 168, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 433 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478987 none COCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 168, 168, 168, 168, 168, 168, 168, 132, 81, 51, 81, 26, 51, 12, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 201, 201, 201, 201, 201, 171, 171, 168, 168, 168, 168, 168, 132, 132, 81, 81, 81, 26, 26, 1, 168, 168, 168, 168, 168, 168] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 827 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478987 none COCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 25, 25, 52, 87, 168, 168, 168, 168, 168, 1, 2, 2, 10, 10, 10, 4, 4, 3, 3, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 52, 52, 168, 1, 1, 2, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 433 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478987 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478987 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478987/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478987 Building REAL300025478988 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478988' /scratch/stefan/7787258/working/building/REAL300025478988 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478988 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478988/0 /scratch/stefan/7787258/working/building/REAL300025478988 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/887 `/scratch/stefan/7787258/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478988 none CC(C)CC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 2, 4, 4, 4, 4, 11, 18, 18, 40, 40, 75, 119, 201, 201, 201, 201, 201, 4, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 18, 18, 18, 75, 75, 201, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 51, 52, 53, 54, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 532 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: REAL300025478988 none CC(C)CC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 177, 201, 177, 177, 177, 161, 105, 66, 105, 27, 66, 13, 1, 1, 1, 1, 1, 1, 1, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 177, 177, 177, 161, 161, 105, 105, 105, 27, 27, 1, 177, 177, 201, 201, 201, 201] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54]) total number of confs: 757 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: REAL300025478988 none CC(C)CC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 12, 12, 28, 28, 61, 100, 177, 177, 177, 177, 177, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 61, 61, 177, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 459 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478988 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478988 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478988/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478988 Building REAL300025478989 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478989' /scratch/stefan/7787258/working/building/REAL300025478989 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478989 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478989/0 /scratch/stefan/7787258/working/building/REAL300025478989 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/888 `/scratch/stefan/7787258/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478989 none COCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 8, 5, 8, 3, 5, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 35, 46, 92, 92, 92, 92, 92, 1, 21, 21, 21, 15, 15, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 35, 35, 92, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 318 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478989 none COCC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 161, 162, 108, 161, 92, 108, 92, 92, 92, 73, 50, 35, 50, 18, 35, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 162, 162, 162, 162, 161, 161, 161, 161, 92, 92, 92, 92, 92, 73, 73, 50, 50, 50, 18, 18, 1, 92, 92] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 955 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478989 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478989 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478989/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478989 Building REAL300025478990 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478990' /scratch/stefan/7787258/working/building/REAL300025478990 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478990 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478990/0 /scratch/stefan/7787258/working/building/REAL300025478990 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/889 `/scratch/stefan/7787258/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478990 none CN(CC1CCN(C(=O)CC2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 14, 32, 32, 32, 32, 32, 1, 9, 11, 11, 17, 17, 41, 41, 41, 41, 41, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 15, 15, 32, 32, 32, 32, 32, 32, 1, 1, 17, 17, 41] 109 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 205 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: REAL300025478990 none CN(CC1CCN(C(=O)CC2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 36, 41, 41, 41, 41, 61, 61, 102, 109, 109, 109, 109, 109, 41, 27, 32, 13, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 36, 36, 41, 41, 41, 41, 41, 102, 102, 109, 109, 109, 109, 109, 109, 41, 41, 27, 27, 1] 109 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 448 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: REAL300025478990 none CN(CC1CCN(C(=O)CC2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [62, 46, 32, 32, 32, 32, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 32, 62, 78, 78, 90, 90, 109, 109, 109, 109, 109, 62, 62, 62, 46, 46, 32, 32, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 32, 32, 90, 90, 109] 109 rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478990 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478990 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478990/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478990 Building REAL300025478991 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478991' /scratch/stefan/7787258/working/building/REAL300025478991 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478991 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478991/0 /scratch/stefan/7787258/working/building/REAL300025478991 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/890 `/scratch/stefan/7787258/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1) `REAL300025478991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478991 none CC1=NC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 11, 11, 17, 17, 17, 17, 39, 51, 51, 54, 54, 86, 127, 201, 201, 201, 201, 201, 17, 1, 2, 2, 2, 1, 6, 6, 17, 17, 17, 17, 17, 39, 39, 51, 51, 51, 86, 86, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 600 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478991 none CC1=NC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 133, 118, 133, 118, 118, 118, 98, 66, 48, 66, 31, 48, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 198, 198, 118, 118, 118, 118, 118, 98, 98, 66, 66, 66, 31, 31, 1, 118, 118] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 857 number of broken/clashed sets: 110 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478991 none CC1=NC=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 11, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 14, 14, 26, 41, 118, 118, 118, 118, 118, 1, 17, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 26, 26, 118, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 110 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478991 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478991 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478991/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478991 Building REAL300025478992 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478992' /scratch/stefan/7787258/working/building/REAL300025478992 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478992 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478992/0 /scratch/stefan/7787258/working/building/REAL300025478992 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/891 `/scratch/stefan/7787258/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2([NH+](C)C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478992 none CN(CC1CCN(C(=O)C2([NH+](C)C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 3, 3, 7, 8, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 7, 7, 9] 9 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 39 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: REAL300025478992 none CN(CC1CCN(C(=O)C2([NH+](C)C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 1] 9 rigid atoms, others: [54, 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, 19, 20, 28, 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: 18 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: REAL300025478992 none CN(CC1CCN(C(=O)C2([NH+](C)C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 1, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9] 9 rigid atoms, others: [48, 7, 9, 10, 44, 45, 14, 15, 16, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51, 52, 53, 54]) total number of confs: 42 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478992 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478992 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478992/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478992 Building REAL300025478993 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478993' /scratch/stefan/7787258/working/building/REAL300025478993 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478993 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478993/0 /scratch/stefan/7787258/working/building/REAL300025478993 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/892 `/scratch/stefan/7787258/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478993 none CC1CCCC1(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 35, 35, 72, 111, 201, 201, 201, 201, 201, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 13, 13, 13, 72, 72, 201, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 519 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478993 none CC1CCCC1(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 126, 71, 126, 27, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 188, 188, 126, 126, 126, 27, 27, 1, 201, 201] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 734 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478993 none CC1CCCC1(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 13, 13, 35, 35, 72, 111, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 72, 72, 201, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 510 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478993 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478993 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478993/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478993 Building REAL300025478994 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478994' /scratch/stefan/7787258/working/building/REAL300025478994 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478994 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478994/0 /scratch/stefan/7787258/working/building/REAL300025478994 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/893 `/scratch/stefan/7787258/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478994 none CN(CC1CCN(C(=O)CC(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 10, 24, 26, 26, 1, 8, 11, 11, 14, 14, 30, 30, 30, 30, 30, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 1, 1, 14, 14, 30] 74 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 185 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478994 none CN(CC1CCN(C(=O)CC(C)(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 26, 27, 30, 30, 30, 30, 37, 37, 60, 73, 74, 74, 30, 21, 25, 12, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 27, 27, 30, 30, 30, 30, 30, 60, 60, 74, 74, 74, 30, 30, 21, 21, 1] 74 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 340 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478994 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478994 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478994/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478994 Building REAL300025478995 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478995' /scratch/stefan/7787258/working/building/REAL300025478995 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478995 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478995/0 /scratch/stefan/7787258/working/building/REAL300025478995 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/894 `/scratch/stefan/7787258/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025478995 none COC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 8, 12, 12, 12, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 30, 52, 153, 153, 153, 153, 153, 1, 10, 10, 10, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 153, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 366 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478995 none COC(CC(C)C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 201, 201, 201, 201, 153, 176, 153, 153, 153, 125, 79, 55, 79, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 125, 125, 79, 79, 79, 28, 28, 1, 153, 153] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 832 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478995 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478995 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478995/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478995 Building REAL300025478996 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478996' /scratch/stefan/7787258/working/building/REAL300025478996 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478996 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478996/0 /scratch/stefan/7787258/working/building/REAL300025478996 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/895 `/scratch/stefan/7787258/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025478996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478996 none CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 1, 1, 2, 2, 3, 3, 3, 3, 7, 12, 12, 27, 27, 58, 100, 201, 201, 201, 201, 201, 3, 1, 1, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 7, 7, 12, 12, 12, 58, 58, 201, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 48, 49, 50, 51, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 483 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478996 none CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 201, 198, 198, 198, 169, 125, 76, 125, 30, 76, 13, 1, 1, 1, 1, 1, 1, 1, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 198, 198, 169, 169, 125, 125, 125, 30, 30, 1, 198, 198, 201, 201, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 740 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478996 none CCCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 26, 26, 57, 98, 198, 198, 198, 198, 198, 1, 3, 3, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 57, 57, 198, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 479 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478996 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478996 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478996/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478996 Building REAL300025478997 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478997' /scratch/stefan/7787258/working/building/REAL300025478997 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478997 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478997/0 /scratch/stefan/7787258/working/building/REAL300025478997 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/896 `/scratch/stefan/7787258/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@]2(C)CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025478997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478997 none CN(CC1CCN(C(=O)[C@]2(C)CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 17, 35, 35, 77, 101, 166, 166, 166, 166, 166, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 77, 77, 166] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 461 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: REAL300025478997 none CN(CC1CCN(C(=O)[C@]2(C)CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 83, 107, 151, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 41, 83, 13, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 151, 151, 166, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 41, 41, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 789 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: REAL300025478997 none CN(CC1CCN(C(=O)[C@]2(C)CCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 30, 50, 50, 100, 131, 201, 201, 201, 201, 201, 30, 30, 30, 14, 14, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 100, 100, 201] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 578 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478997 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478997 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478997/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478997 Building REAL300025478998 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478998' /scratch/stefan/7787258/working/building/REAL300025478998 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478998 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478998/0 /scratch/stefan/7787258/working/building/REAL300025478998 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/897 `/scratch/stefan/7787258/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478998 none CCC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 14, 18, 18, 23, 23, 46, 64, 118, 118, 118, 118, 118, 7, 3, 3, 3, 2, 2, 1, 7, 7, 7, 7, 7, 14, 14, 18, 18, 18, 46, 46, 118, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 332 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478998 none CCC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 118, 118, 118, 118, 118, 95, 71, 95, 71, 71, 71, 62, 41, 31, 41, 21, 31, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 118, 71, 71, 71, 71, 71, 62, 62, 41, 41, 41, 21, 21, 1, 71, 71] 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, 46, 47]) total number of confs: 901 number of broken/clashed sets: 121 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478998 none CCC1=NOC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 7, 7, 9, 9, 22, 31, 71, 71, 71, 71, 71, 1, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 22, 22, 71, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 210 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478998 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478998 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478998/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478998 Building REAL300025478999 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025478999' /scratch/stefan/7787258/working/building/REAL300025478999 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025478999 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025478999/0 /scratch/stefan/7787258/working/building/REAL300025478999 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/898 `/scratch/stefan/7787258/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025478999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025478999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025478999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025478999 none CC1COCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 16, 30, 30, 53, 53, 86, 129, 201, 201, 201, 201, 201, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 30, 30, 30, 86, 86, 201, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 569 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478999 none CC1COCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 186, 201, 186, 186, 186, 163, 107, 69, 107, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 186, 186, 163, 163, 107, 107, 107, 29, 29, 1, 186, 186] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 762 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025478999 none CC1COCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 26, 26, 56, 88, 186, 186, 186, 186, 186, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 56, 56, 186, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 447 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025478999 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025478999 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025478999/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025478999 Building REAL300025479000 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479000' /scratch/stefan/7787258/working/building/REAL300025479000 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479000 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479000/0 /scratch/stefan/7787258/working/building/REAL300025479000 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/899 `/scratch/stefan/7787258/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1C) `REAL300025479000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479000 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 27, 37, 37, 51, 51, 77, 121, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 27, 27, 37, 37, 37, 77, 77, 201, 10, 10, 1, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 45, 46, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 553 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479000 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 137, 163, 137, 137, 137, 114, 84, 64, 84, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 137, 137, 114, 114, 84, 84, 84, 29, 29, 1, 137, 137, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 686 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479000 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 41, 65, 137, 137, 137, 137, 137, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 41, 41, 137, 1, 1, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 340 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479000 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479000 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479000/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479000 Building REAL300025479001 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479001' /scratch/stefan/7787258/working/building/REAL300025479001 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479001 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479001/0 /scratch/stefan/7787258/working/building/REAL300025479001 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/900 `/scratch/stefan/7787258/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(Cl)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479001 none CN(CC1CCN(C(=O)C2=CC=C(Cl)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 1, 13, 23, 23, 46, 65, 122, 122, 122, 122, 122, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 46, 46, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 324 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479001 none CN(CC1CCN(C(=O)C2=CC=C(Cl)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 62, 65, 105, 122, 122, 122, 122, 144, 144, 201, 201, 201, 201, 201, 122, 37, 62, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 105, 105, 122, 122, 122, 122, 122, 201, 201, 201, 122, 122, 37, 37, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 699 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: REAL300025479001 none CN(CC1CCN(C(=O)C2=CC=C(Cl)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 40, 64, 64, 107, 135, 201, 201, 201, 201, 201, 40, 40, 40, 26, 26, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 107, 107, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 600 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479001 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479001 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479001/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479001 Building REAL300025479002 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479002' /scratch/stefan/7787258/working/building/REAL300025479002 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479002 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479002/0 /scratch/stefan/7787258/working/building/REAL300025479002 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/901 `/scratch/stefan/7787258/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479002 none COCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 16, 10, 3, 10, 14, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 26, 37, 90, 90, 90, 90, 90, 1, 29, 29, 29, 16, 16, 10, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 26, 26, 90, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 297 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479002 none COCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 93, 173, 176, 90, 93, 90, 90, 90, 79, 61, 40, 61, 20, 40, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 173, 176, 176, 176, 90, 90, 90, 90, 90, 79, 79, 61, 61, 61, 20, 20, 1, 90, 90] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 900 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479002 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479002 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479002/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479002 Building REAL300025479003 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479003' /scratch/stefan/7787258/working/building/REAL300025479003 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479003 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479003/0 /scratch/stefan/7787258/working/building/REAL300025479003 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/902 `/scratch/stefan/7787258/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479003 none CN(CC1CCN(C(=O)C2CCC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 1, 11, 28, 28, 53, 68, 116, 116, 116, 116, 116, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 53, 53, 116] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479003 none CN(CC1CCN(C(=O)C2CCC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 63, 73, 101, 116, 116, 116, 116, 122, 122, 201, 201, 201, 201, 201, 201, 116, 35, 63, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 101, 101, 116, 116, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 35, 35, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 807 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: REAL300025479003 none CN(CC1CCN(C(=O)C2CCC(C)(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 15, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 28, 58, 58, 104, 128, 201, 201, 201, 201, 201, 28, 28, 28, 15, 15, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 7, 104, 104, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 48, 49, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54]) total number of confs: 612 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479003 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479003 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479003/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479003 Building REAL300025479004 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479004' /scratch/stefan/7787258/working/building/REAL300025479004 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479004 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479004/0 /scratch/stefan/7787258/working/building/REAL300025479004 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/903 `/scratch/stefan/7787258/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1) `REAL300025479004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479004 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 38, 56, 156, 156, 156, 156, 156, 1, 7, 11, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 38, 38, 156, 1, 1, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 369 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479004 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 7, 11, 11, 11, 11, 22, 31, 31, 37, 37, 66, 100, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 11, 11, 22, 22, 31, 31, 31, 66, 66, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 514 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479004 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 156, 169, 156, 156, 156, 132, 100, 58, 100, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 132, 132, 100, 100, 100, 28, 28, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 814 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479004 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479004 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479004/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479004 Building REAL300025479005 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479005' /scratch/stefan/7787258/working/building/REAL300025479005 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479005 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479005/0 /scratch/stefan/7787258/working/building/REAL300025479005 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/904 `/scratch/stefan/7787258/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479005 none CCC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 21, 27, 27, 27, 27, 54, 81, 157, 157, 157, 157, 157, 12, 8, 8, 8, 8, 8, 6, 6, 1, 1, 12, 12, 12, 12, 12, 21, 21, 27, 27, 27, 54, 54, 157, 12, 12] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 3, 36] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 435 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479005 none CCC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 157, 157, 157, 100, 157, 100, 100, 100, 100, 100, 84, 46, 43, 46, 29, 43, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 157, 157, 100, 100, 100, 100, 100, 84, 84, 46, 46, 46, 29, 29, 1, 100, 100] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 871 number of broken/clashed sets: 157 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479005 none CCC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 12, 12, 12, 12, 2, 12, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 17, 27, 100, 100, 100, 100, 100, 1, 27, 27, 27, 27, 27, 26, 26, 12, 12, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 17, 17, 100, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 40, 50, 51, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479005 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479005 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479005/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479005 Building REAL300025479006 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479006' /scratch/stefan/7787258/working/building/REAL300025479006 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479006 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479006/0 /scratch/stefan/7787258/working/building/REAL300025479006 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/905 `/scratch/stefan/7787258/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C23CC2CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479006 none CN(CC1CCN(C(=O)C23CC2CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 14, 36, 36, 87, 114, 171, 171, 171, 171, 171, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 87, 87, 171] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 488 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479006 none CN(CC1CCN(C(=O)C23CC2CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 69, 100, 147, 171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 171, 39, 69, 13, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 147, 147, 171, 171, 171, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 39, 39, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 818 number of broken/clashed sets: 97 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479006 none CN(CC1CCN(C(=O)C23CC2CCCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 23, 48, 48, 104, 138, 201, 201, 201, 201, 201, 23, 23, 23, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 104, 104, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 577 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479006 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479006 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479006/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479006 Building REAL300025479007 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479007' /scratch/stefan/7787258/working/building/REAL300025479007 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479007 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479007/0 /scratch/stefan/7787258/working/building/REAL300025479007 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/906 `/scratch/stefan/7787258/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025479007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479007 none CC(C)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 4, 4, 6, 6, 6, 6, 12, 18, 18, 37, 37, 68, 110, 201, 201, 201, 201, 201, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 12, 12, 18, 18, 18, 68, 68, 201, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 48, 49, 50, 51, 24, 25] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479007 none CC(C)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 186, 200, 186, 186, 186, 161, 115, 68, 115, 29, 68, 13, 1, 1, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 186, 186, 161, 161, 115, 115, 115, 29, 29, 1, 186, 186, 201, 201, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 751 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479007 none CC(C)C1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 5, 1, 5, 1, 1, 1, 1, 1, 6, 12, 12, 31, 31, 59, 99, 186, 186, 186, 186, 186, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 59, 59, 186, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 476 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479007 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479007 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479007/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479007 Building REAL300025479008 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479008' /scratch/stefan/7787258/working/building/REAL300025479008 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479008 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479008/0 /scratch/stefan/7787258/working/building/REAL300025479008 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/907 `/scratch/stefan/7787258/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479008 none C=C1CC(C)(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 11, 21, 21, 47, 47, 74, 119, 201, 201, 201, 201, 201, 4, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 21, 21, 21, 74, 74, 201, 4, 4, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 516 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: REAL300025479008 none C=C1CC(C)(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 174, 201, 174, 174, 174, 156, 103, 58, 103, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 174, 156, 156, 103, 103, 103, 27, 27, 1, 174, 174, 201, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 787 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: REAL300025479008 none C=C1CC(C)(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 14, 14, 35, 35, 61, 98, 174, 174, 174, 174, 174, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 61, 61, 174, 1, 1, 4, 4] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 438 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479008 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479008 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479008/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479008 Building REAL300025479009 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479009' /scratch/stefan/7787258/working/building/REAL300025479009 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479009 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479009/0 /scratch/stefan/7787258/working/building/REAL300025479009 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/908 `/scratch/stefan/7787258/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(C)C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479009 none CN(CC1CCN(C(=O)C(C)(C)C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 20, 20, 1, 10, 14, 14, 21, 21, 47, 47, 47, 47, 47, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 20, 1, 1, 21, 21, 47] 124 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479009 none CN(CC1CCN(C(=O)C(C)(C)C(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 39, 42, 47, 47, 47, 47, 81, 81, 121, 121, 121, 124, 124, 47, 30, 37, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 42, 42, 47, 47, 47, 47, 47, 121, 121, 121, 121, 121, 121, 124, 47, 47, 30, 30, 1] 124 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 491 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479009 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479009 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479009/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479009 Building REAL300025479010 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479010' /scratch/stefan/7787258/working/building/REAL300025479010 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479010 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479010/0 /scratch/stefan/7787258/working/building/REAL300025479010 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/909 `/scratch/stefan/7787258/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1) `REAL300025479010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479010 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 10, 10, 13, 13, 13, 13, 25, 33, 33, 44, 44, 73, 112, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 6, 6, 13, 13, 13, 13, 13, 25, 25, 33, 33, 33, 73, 73, 201, 13, 13, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 47, 48, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 548 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: REAL300025479010 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 136, 115, 136, 115, 115, 115, 108, 70, 49, 70, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 189, 189, 115, 115, 115, 115, 115, 108, 108, 70, 70, 70, 28, 28, 1, 115, 115, 201, 201] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 838 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: REAL300025479010 none CC1=C(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 36, 58, 115, 115, 115, 115, 115, 1, 13, 13, 13, 13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 36, 36, 115, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 326 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479010 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479010 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479010/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479010 Building REAL300025479011 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479011' /scratch/stefan/7787258/working/building/REAL300025479011 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479011 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479011/0 /scratch/stefan/7787258/working/building/REAL300025479011 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/910 `/scratch/stefan/7787258/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1) `REAL300025479011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479011 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 17, 24, 24, 29, 29, 59, 87, 179, 179, 179, 179, 179, 6, 1, 1, 1, 4, 4, 4, 3, 3, 6, 6, 6, 6, 6, 17, 17, 24, 24, 24, 59, 59, 179, 6, 6, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 472 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479011 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 179, 144, 116, 144, 116, 116, 116, 100, 62, 46, 62, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 116, 179, 179, 179, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 100, 100, 62, 62, 62, 26, 26, 1, 116, 116, 179] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 112 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479011 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 28, 45, 116, 116, 116, 116, 116, 1, 7, 7, 7, 15, 15, 15, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 28, 28, 116, 1, 1, 7] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 310 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479011 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479011 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479011/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479011 Building REAL300025479012 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479012' /scratch/stefan/7787258/working/building/REAL300025479012 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479012 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479012/0 /scratch/stefan/7787258/working/building/REAL300025479012 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/911 `/scratch/stefan/7787258/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(CF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479012 none CN(CC1CCN(C(=O)C2(CF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 6, 14, 6, 6, 1, 5, 7, 7, 8, 8, 14, 14, 14, 14, 14, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 14, 14, 6, 6, 6, 6, 1, 1, 8, 8, 14] 24 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479012 none CN(CC1CCN(C(=O)C2(CF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 14, 14, 14, 14, 20, 20, 24, 24, 24, 24, 14, 13, 13, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 24, 14, 14, 13, 13, 1] 24 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479012 none CN(CC1CCN(C(=O)C2(CF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 6, 6, 6, 6, 3, 1, 3, 1, 1, 8, 1, 1, 6, 11, 15, 15, 17, 17, 24, 24, 24, 24, 24, 11, 11, 11, 9, 9, 6, 6, 6, 6, 6, 8, 8, 1, 1, 1, 1, 6, 6, 17, 17, 24] 24 rigid atoms, others: [37, 38, 7, 40, 9, 10, 39, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 14, 15, 16, 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]) total number of confs: 100 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479012 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479012 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479012/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479012 Building REAL300025479013 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479013' /scratch/stefan/7787258/working/building/REAL300025479013 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479013 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479013/0 /scratch/stefan/7787258/working/building/REAL300025479013 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/912 `/scratch/stefan/7787258/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC3(CC3)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479013 none CN(CC1CCN(C(=O)C2CC3(CC3)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 1, 12, 27, 27, 48, 64, 118, 118, 118, 118, 118, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 48, 48, 118] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 328 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: REAL300025479013 none CN(CC1CCN(C(=O)C2CC3(CC3)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 66, 74, 105, 118, 118, 118, 118, 122, 122, 201, 201, 201, 201, 201, 118, 39, 66, 13, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 105, 105, 118, 118, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 118, 39, 39, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 803 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: REAL300025479013 none CN(CC1CCN(C(=O)C2CC3(CC3)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 21, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 36, 67, 67, 102, 129, 201, 201, 201, 201, 201, 36, 36, 36, 21, 21, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 102, 102, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 599 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479013 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479013 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479013/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479013 Building REAL300025479014 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479014' /scratch/stefan/7787258/working/building/REAL300025479014 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479014 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479014/0 /scratch/stefan/7787258/working/building/REAL300025479014 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/913 `/scratch/stefan/7787258/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1) `REAL300025479014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479014 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 19, 19, 43, 70, 144, 144, 144, 144, 144, 1, 4, 9, 9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 43, 43, 144, 1, 1, 9, 9, 9] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 44, 34, 45, 21, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 364 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479014 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 6, 6, 9, 9, 9, 9, 20, 28, 28, 40, 40, 78, 118, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 9, 20, 20, 28, 28, 28, 78, 78, 201, 9, 9, 1, 1, 1] 201 rigid atoms, others: [1, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 556 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: REAL300025479014 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 144, 183, 144, 144, 144, 135, 82, 56, 82, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 144, 183, 201, 201, 201, 201, 183, 183, 183, 183, 144, 144, 144, 144, 144, 135, 135, 82, 82, 82, 26, 26, 1, 144, 144, 201, 201, 201] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 748 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479014 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479014 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479014/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479014 Building REAL300025479015 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479015' /scratch/stefan/7787258/working/building/REAL300025479015 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479015 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479015/0 /scratch/stefan/7787258/working/building/REAL300025479015 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/914 `/scratch/stefan/7787258/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479015 none CN(CC1CCN(C(=O)C2(C)CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 16, 41, 41, 87, 121, 190, 190, 190, 190, 190, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 87, 87, 190] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 515 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479015 none CN(CC1CCN(C(=O)C2(C)CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 86, 121, 171, 190, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 39, 86, 13, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 171, 171, 190, 190, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 39, 39, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 793 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479015 none CN(CC1CCN(C(=O)C2(C)CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 22, 49, 49, 94, 132, 201, 201, 201, 201, 201, 22, 22, 22, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 94, 94, 201] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 547 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479015 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479015 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479015/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479015 Building REAL300025479016 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479016' /scratch/stefan/7787258/working/building/REAL300025479016 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479016 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479016/0 /scratch/stefan/7787258/working/building/REAL300025479016 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/915 `/scratch/stefan/7787258/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479016 none CC1CCC[N@@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 14, 14, 14, 14, 22, 25, 25, 34, 34, 78, 119, 191, 191, 191, 191, 191, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 22, 22, 25, 25, 25, 78, 78, 191, 14, 14] 191 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 531 number of broken/clashed sets: 127 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479016 none CC1CCC[N@@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [191, 191, 191, 191, 191, 191, 191, 131, 126, 131, 126, 126, 126, 100, 89, 72, 89, 34, 72, 13, 1, 1, 1, 1, 1, 1, 1, 126, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 126, 126, 126, 126, 126, 100, 100, 89, 89, 89, 34, 34, 1, 126, 126] 191 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 818 number of broken/clashed sets: 127 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479016 none CC1CCC[N@@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 14, 9, 14, 4, 1, 4, 1, 1, 1, 1, 1, 4, 6, 6, 9, 9, 24, 44, 126, 126, 126, 126, 126, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 24, 24, 126, 1, 1] 191 rigid atoms, others: [43, 8, 41, 10, 11, 12, 13, 14, 44, 40, 53, 54, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 127 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479016 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479016/1 /scratch/stefan/7787258/working/building/REAL300025479016 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/916 `/scratch/stefan/7787258/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479016.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479016 none CC1CCC[N@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 17, 17, 17, 17, 26, 28, 28, 36, 36, 74, 119, 201, 201, 201, 201, 201, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 26, 26, 28, 28, 28, 74, 74, 201, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 537 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479016 none CC1CCC[N@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 197, 201, 127, 125, 127, 125, 125, 125, 89, 84, 66, 84, 34, 66, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 125, 125, 125, 125, 125, 89, 89, 84, 84, 84, 34, 34, 1, 125, 125] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 834 number of broken/clashed sets: 145 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479016 none CC1CCC[N@H+]1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 10, 17, 3, 1, 3, 1, 1, 1, 1, 1, 4, 6, 6, 9, 9, 21, 34, 125, 125, 125, 125, 125, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 21, 21, 125, 1, 1] 201 rigid atoms, others: [43, 8, 41, 10, 11, 12, 13, 14, 44, 40, 53, 54, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 278 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479016 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479016 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479016/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479016/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479016 Building REAL300025479017 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479017' /scratch/stefan/7787258/working/building/REAL300025479017 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479017 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479017/0 /scratch/stefan/7787258/working/building/REAL300025479017 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/917 `/scratch/stefan/7787258/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479017 none CN(CC1CCN(C(=O)C2=CNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 10, 10, 1, 13, 28, 28, 46, 63, 100, 100, 100, 100, 100, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 46, 46, 100] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479017 none CN(CC1CCN(C(=O)C2=CNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 59, 65, 95, 100, 100, 100, 100, 110, 110, 201, 201, 201, 201, 201, 201, 100, 37, 59, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 95, 95, 100, 100, 100, 100, 100, 201, 201, 201, 201, 100, 100, 37, 37, 1] 201 rigid atoms, others: [45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 621 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479017 none CN(CC1CCN(C(=O)C2=CNC(=O)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 25, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 46, 73, 73, 107, 137, 201, 201, 201, 201, 201, 46, 46, 46, 25, 25, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 107, 107, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 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]) total number of confs: 586 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479017 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479017 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479017/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479017 Building REAL300025479018 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479018' /scratch/stefan/7787258/working/building/REAL300025479018 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479018 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479018/0 /scratch/stefan/7787258/working/building/REAL300025479018 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/918 `/scratch/stefan/7787258/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479018 none CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 23, 37, 101, 101, 101, 101, 101, 1, 15, 15, 15, 15, 15, 14, 14, 15, 15, 14, 14, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 101, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 267 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479018 none CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 111, 101, 111, 101, 101, 101, 89, 64, 48, 64, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 101, 101, 101, 101, 101, 89, 89, 64, 64, 64, 28, 28, 1, 101, 101] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 882 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479018 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479018 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479018/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479018 Building REAL300025479019 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479019' /scratch/stefan/7787258/working/building/REAL300025479019 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479019 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479019/0 /scratch/stefan/7787258/working/building/REAL300025479019 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/919 `/scratch/stefan/7787258/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479019 none CC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 3, 5, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 23, 23, 53, 87, 183, 183, 183, 183, 183, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 53, 53, 183, 1, 1] 201 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 438 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479019 none CC(C)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 183, 201, 183, 183, 183, 168, 110, 71, 110, 28, 71, 13, 1, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 183, 168, 168, 110, 110, 110, 28, 28, 1, 183, 183] 201 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 756 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479019 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479019 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479019/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479019 Building REAL300025479020 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479020' /scratch/stefan/7787258/working/building/REAL300025479020 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479020 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479020/0 /scratch/stefan/7787258/working/building/REAL300025479020 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/920 `/scratch/stefan/7787258/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479020 none CC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 20, 31, 31, 48, 48, 78, 123, 201, 201, 201, 201, 201, 8, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 31, 31, 31, 78, 78, 201, 8, 8, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 50, 51, 25, 5, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 553 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479020 none CC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 151, 140, 151, 140, 140, 140, 126, 85, 55, 85, 27, 55, 13, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 126, 126, 85, 85, 85, 27, 27, 1, 140, 140, 201, 201] 201 rigid atoms, others: [47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51]) total number of confs: 795 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479020 none CC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 38, 64, 140, 140, 140, 140, 140, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 38, 38, 140, 1, 1, 8, 8] 201 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 48, 49, 24, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 335 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479020 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479020 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479020/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479020 Building REAL300025479021 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479021' /scratch/stefan/7787258/working/building/REAL300025479021 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479021 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479021/0 /scratch/stefan/7787258/working/building/REAL300025479021 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/921 `/scratch/stefan/7787258/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025479021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479021 none CCN1C=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 6, 14, 19, 19, 23, 23, 45, 67, 159, 159, 159, 159, 159, 5, 1, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 14, 14, 19, 19, 19, 45, 45, 159, 5, 5] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 373 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479021 none CCN1C=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 159, 159, 159, 156, 139, 156, 139, 139, 139, 122, 80, 55, 80, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 139, 159, 201, 201, 201, 201, 201, 159, 159, 139, 139, 139, 139, 139, 122, 122, 80, 80, 80, 30, 30, 1, 139, 139] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 858 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479021 none CCN1C=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 30, 46, 139, 139, 139, 139, 139, 1, 6, 12, 12, 12, 12, 12, 6, 5, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 30, 30, 139, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 320 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479021 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479021 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479021/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479021 Building REAL300025479022 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479022' /scratch/stefan/7787258/working/building/REAL300025479022 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479022 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479022/0 /scratch/stefan/7787258/working/building/REAL300025479022 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/922 `/scratch/stefan/7787258/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C) `REAL300025479022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479022 none CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 12, 12, 27, 46, 112, 112, 112, 112, 112, 1, 6, 10, 10, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 27, 27, 112, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 294 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479022 none CCOC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 124, 112, 124, 112, 112, 112, 97, 61, 46, 61, 25, 46, 13, 1, 1, 1, 1, 1, 1, 1, 112, 200, 201, 201, 200, 200, 200, 200, 200, 200, 112, 112, 112, 112, 112, 97, 97, 61, 61, 61, 25, 25, 1, 112, 112, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 951 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479022 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479022 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479022/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479022 Building REAL300025479023 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479023' /scratch/stefan/7787258/working/building/REAL300025479023 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479023 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479023/0 /scratch/stefan/7787258/working/building/REAL300025479023 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/923 `/scratch/stefan/7787258/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479023 none C#CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 29, 12, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 18, 18, 23, 28, 56, 56, 56, 56, 56, 1, 62, 62, 62, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 23, 23, 56, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 355 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479023 none C#CCOCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 119, 119, 69, 56, 69, 56, 56, 56, 44, 37, 29, 37, 17, 29, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 119, 119, 119, 119, 56, 56, 56, 56, 56, 44, 44, 37, 37, 37, 17, 17, 1, 56, 56] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 802 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479023 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479023 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479023/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479023 Building REAL300025479024 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479024' /scratch/stefan/7787258/working/building/REAL300025479024 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479024 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479024/0 /scratch/stefan/7787258/working/building/REAL300025479024 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/924 `/scratch/stefan/7787258/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479024 none C#CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 23, 41, 124, 124, 124, 124, 124, 1, 22, 22, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 124, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 330 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479024 none C#CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 150, 139, 150, 124, 139, 124, 124, 124, 100, 64, 47, 64, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 150, 150, 150, 150, 124, 124, 124, 124, 124, 100, 100, 64, 64, 64, 27, 27, 1, 124, 124] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 814 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479024 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479024 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479024/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479024 Building REAL300025479025 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479025' /scratch/stefan/7787258/working/building/REAL300025479025 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479025 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479025/0 /scratch/stefan/7787258/working/building/REAL300025479025 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/925 `/scratch/stefan/7787258/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCOCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479025 none CN(CC1CCN(C(=O)CCOCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 12, 19, 40, 58, 58, 1, 8, 11, 11, 16, 16, 47, 47, 47, 47, 47, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 10, 9, 11, 11, 39, 39, 58, 58, 58, 58, 58, 1, 1, 16, 16, 47] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 315 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479025 none CN(CC1CCN(C(=O)CCOCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 39, 42, 47, 47, 47, 47, 66, 66, 112, 113, 132, 193, 201, 201, 47, 31, 37, 13, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 42, 42, 47, 47, 47, 47, 47, 112, 112, 113, 113, 193, 193, 201, 201, 201, 201, 201, 47, 47, 31, 31, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 845 number of broken/clashed sets: 104 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479025 none CN(CC1CCN(C(=O)CCOCC2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 85, 58, 58, 58, 58, 47, 29, 47, 23, 14, 6, 1, 1, 1, 1, 58, 121, 153, 153, 162, 162, 201, 201, 201, 201, 201, 121, 121, 121, 85, 85, 58, 58, 58, 58, 58, 29, 29, 23, 23, 6, 6, 1, 1, 1, 1, 1, 58, 58, 162, 162, 201] 201 rigid atoms, others: [45, 12, 43, 44, 13, 14, 15, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 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, 48, 49, 50, 51, 52]) total number of confs: 698 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479025 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479025 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479025/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479025 Building REAL300025479026 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479026' /scratch/stefan/7787258/working/building/REAL300025479026 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479026 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479026/0 /scratch/stefan/7787258/working/building/REAL300025479026 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/926 `/scratch/stefan/7787258/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(C)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479026 none CN(CC1CCN(C(=O)C(C)(C)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 1, 16, 30, 30, 53, 69, 116, 116, 116, 116, 116, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 7, 7, 1, 1, 53, 53, 116] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479026 none CN(CC1CCN(C(=O)C(C)(C)C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 57, 71, 105, 116, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 116, 32, 57, 13, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 105, 105, 116, 116, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 32, 32, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 756 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479026 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479026 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479026/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479026 Building REAL300025479027 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479027' /scratch/stefan/7787258/working/building/REAL300025479027 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479027 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479027/0 /scratch/stefan/7787258/working/building/REAL300025479027 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/927 `/scratch/stefan/7787258/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025479027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479027 none CC(C)[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 4, 6, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 13, 22, 70, 70, 70, 70, 70, 1, 6, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 70, 1, 1, 10, 10, 10, 10, 10, 10] 105 rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 40, 50, 24, 49, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54, 55, 56]) total number of confs: 194 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479027 none CC(C)[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 92, 105, 92, 92, 70, 92, 70, 70, 70, 54, 54, 47, 54, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 70, 92, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 70, 70, 70, 70, 70, 54, 54, 54, 54, 54, 29, 29, 1, 70, 70, 105, 105, 105, 105, 105, 105] 105 rigid atoms, others: [48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 497 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479027 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479027 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479027/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479027 Building REAL300025479028 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479028' /scratch/stefan/7787258/working/building/REAL300025479028 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479028 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479028/0 /scratch/stefan/7787258/working/building/REAL300025479028 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/928 `/scratch/stefan/7787258/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1) `REAL300025479028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479028 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 22, 32, 32, 54, 54, 80, 123, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 22, 22, 32, 32, 32, 80, 80, 201, 7, 7, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 48, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 564 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: REAL300025479028 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 122, 162, 122, 122, 122, 107, 76, 54, 76, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 122, 122, 107, 107, 76, 76, 76, 28, 28, 1, 122, 122, 201, 201, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 681 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: REAL300025479028 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 5, 9, 9, 23, 23, 40, 63, 122, 122, 122, 122, 122, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 40, 40, 122, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 315 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479028 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479028 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479028/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479028 Building REAL300025479029 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479029' /scratch/stefan/7787258/working/building/REAL300025479029 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479029 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479029/0 /scratch/stefan/7787258/working/building/REAL300025479029 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/929 `/scratch/stefan/7787258/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479029 none CN(CC1CCN(C(=O)CC2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 18, 42, 42, 42, 42, 1, 9, 14, 14, 22, 22, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 18, 18, 42, 42, 1, 1, 22, 22, 50] 179 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479029 none CN(CC1CCN(C(=O)CC2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [39, 38, 39, 42, 50, 50, 50, 50, 59, 59, 126, 179, 179, 179, 179, 50, 29, 38, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 42, 42, 50, 50, 50, 50, 50, 126, 126, 179, 179, 50, 50, 29, 29, 1] 179 rigid atoms, others: [44, 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]) total number of confs: 600 number of broken/clashed sets: 106 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479029 none CN(CC1CCN(C(=O)CC2=CN=CS2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 14, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [97, 71, 42, 42, 42, 42, 19, 4, 20, 1, 1, 1, 1, 1, 1, 42, 97, 118, 118, 136, 136, 179, 179, 179, 179, 179, 97, 97, 97, 71, 71, 42, 42, 42, 42, 42, 4, 4, 1, 1, 42, 42, 136, 136, 179] 179 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 592 number of broken/clashed sets: 106 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479029 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479029 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479029/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479029 Building REAL300025479030 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479030' /scratch/stefan/7787258/working/building/REAL300025479030 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479030 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479030/0 /scratch/stefan/7787258/working/building/REAL300025479030 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/930 `/scratch/stefan/7787258/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(=O)NN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479030 none CN(CC1CCN(C(=O)C2=CC(=O)NN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 13, 1, 13, 26, 26, 48, 69, 117, 117, 117, 117, 117, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 13, 13, 13, 1, 1, 48, 48, 117] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479030 none CN(CC1CCN(C(=O)C2=CC(=O)NN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 56, 64, 99, 117, 117, 117, 117, 138, 138, 201, 201, 201, 201, 201, 201, 117, 35, 56, 13, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 99, 99, 117, 117, 117, 117, 117, 201, 201, 201, 117, 117, 35, 35, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 689 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479030 none CN(CC1CCN(C(=O)C2=CC(=O)NN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 31, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 13, 52, 80, 80, 121, 149, 201, 201, 201, 201, 201, 52, 52, 52, 31, 31, 13, 13, 13, 13, 13, 1, 1, 1, 13, 13, 121, 121, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 636 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479030 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479030 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479030/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479030 Building REAL300025479031 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479031' /scratch/stefan/7787258/working/building/REAL300025479031 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479031 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479031/0 /scratch/stefan/7787258/working/building/REAL300025479031 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/931 `/scratch/stefan/7787258/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1) `REAL300025479031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479031 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 28, 39, 39, 54, 54, 86, 125, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 28, 28, 39, 39, 39, 86, 86, 201, 9, 9, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 45, 46, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 582 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: REAL300025479031 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 119, 151, 119, 119, 119, 99, 73, 58, 73, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 99, 99, 73, 73, 73, 28, 28, 1, 119, 119, 201, 201] 201 rigid atoms, others: [42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 673 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: REAL300025479031 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 36, 53, 119, 119, 119, 119, 119, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 36, 36, 119, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 43, 44, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 289 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479031 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479031 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479031/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479031 Building REAL300025479032 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479032' /scratch/stefan/7787258/working/building/REAL300025479032 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479032 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479032/0 /scratch/stefan/7787258/working/building/REAL300025479032 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/932 `/scratch/stefan/7787258/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C3CC3)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025479032 none CN(CC1CCN(C(=O)C2(C3CC3)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 3, 3, 1, 6, 8, 8, 8, 8, 10, 10, 10, 10, 10, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 3, 3, 3, 1, 1, 8, 8, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479032 none CN(CC1CCN(C(=O)C2(C3CC3)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 9, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 1] 10 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 22 number of broken/clashed sets: 7 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479032 none CN(CC1CCN(C(=O)C2(C3CC3)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 6, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 10, 10, 10] 10 rigid atoms, others: [36, 37, 38, 39, 40, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 32 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: REAL300025479032 none CN(CC1CCN(C(=O)C2(C3CC3)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 3, 3, 1, 1, 3, 7, 9, 9, 9, 9, 10, 10, 10, 10, 10, 7, 7, 7, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 9, 9, 10] 10 rigid atoms, others: [7, 9, 10, 43, 44, 13, 14, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479032 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479032 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479032/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479032 Building REAL300025479033 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479033' /scratch/stefan/7787258/working/building/REAL300025479033 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479033 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479033/0 /scratch/stefan/7787258/working/building/REAL300025479033 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/933 `/scratch/stefan/7787258/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479033 none COC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 21, 30, 30, 31, 31, 64, 93, 201, 201, 201, 201, 201, 11, 1, 4, 4, 4, 1, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 30, 30, 30, 64, 64, 201, 11, 11, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 48, 49, 25, 29, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 510 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479033 none COC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 124, 116, 124, 116, 116, 116, 93, 53, 47, 53, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 93, 93, 53, 53, 53, 29, 29, 1, 116, 116, 201, 201] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 734 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479033 none COC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 20, 35, 116, 116, 116, 116, 116, 1, 11, 22, 22, 22, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 20, 20, 116, 1, 1, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 270 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479033 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479033 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479033/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479033 Building REAL300025479034 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479034' /scratch/stefan/7787258/working/building/REAL300025479034 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479034 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479034/0 /scratch/stefan/7787258/working/building/REAL300025479034 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/934 `/scratch/stefan/7787258/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CCCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479034 none CN(CC1CCN(C(=O)[C@H]2CCCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 15, 35, 35, 72, 99, 170, 170, 170, 170, 170, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 72, 72, 170] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 462 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479034 none CN(CC1CCN(C(=O)[C@H]2CCCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 84, 106, 149, 170, 170, 170, 170, 186, 186, 201, 201, 201, 201, 201, 201, 201, 170, 41, 84, 13, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 149, 149, 170, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 170, 170, 41, 41, 1] 201 rigid atoms, others: [49, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 788 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479034 none CN(CC1CCN(C(=O)[C@H]2CCCC(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 59, 59, 101, 131, 201, 201, 201, 201, 201, 32, 32, 32, 17, 17, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 101, 101, 201] 201 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 45, 46, 47, 48, 49]) total number of confs: 566 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479034 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479034 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479034/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479034 Building REAL300025479035 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479035' /scratch/stefan/7787258/working/building/REAL300025479035 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479035 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479035/0 /scratch/stefan/7787258/working/building/REAL300025479035 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/935 `/scratch/stefan/7787258/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479035 none CC1CC[N@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 15, 15, 15, 15, 23, 27, 27, 37, 37, 79, 130, 201, 201, 201, 201, 201, 15, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 23, 23, 27, 27, 27, 79, 79, 201, 15, 15, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 561 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479035 none CC1CC[N@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 201, 127, 124, 127, 124, 124, 124, 88, 75, 62, 75, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 124, 124, 124, 124, 124, 88, 88, 75, 75, 75, 31, 31, 1, 124, 124, 201, 201] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 853 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479035 none CC1CC[N@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 8, 15, 3, 1, 3, 1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 19, 37, 124, 124, 124, 124, 124, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 19, 19, 124, 1, 1, 15, 15] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 264 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479035 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479035/1 /scratch/stefan/7787258/working/building/REAL300025479035 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/936 `/scratch/stefan/7787258/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479035.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479035 none CC1CC[N@@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 16, 16, 16, 16, 26, 30, 30, 41, 41, 81, 130, 201, 201, 201, 201, 201, 16, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 26, 26, 30, 30, 30, 81, 81, 201, 16, 16, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 35, 53, 54, 27, 5, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 578 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479035 none CC1CC[N@@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 183, 201, 124, 123, 124, 123, 123, 123, 84, 76, 65, 76, 32, 65, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 123, 123, 123, 123, 123, 84, 84, 76, 76, 76, 32, 32, 1, 123, 123, 201, 201] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54]) total number of confs: 843 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479035 none CC1CC[N@@H+](CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 8, 16, 3, 1, 3, 1, 1, 1, 1, 1, 3, 4, 4, 7, 7, 18, 33, 123, 123, 123, 123, 123, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 18, 18, 123, 1, 1, 16, 16] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54]) total number of confs: 261 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479035 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479035 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479035/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479035/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479035 Building REAL300025479036 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479036' /scratch/stefan/7787258/working/building/REAL300025479036 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479036 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479036/0 /scratch/stefan/7787258/working/building/REAL300025479036 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/937 `/scratch/stefan/7787258/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479036 none CN(CC1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 6, 6, 1, 5, 6, 6, 8, 8, 12, 12, 12, 12, 12, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 4, 4, 6, 6, 1, 1, 8, 8, 12] 13 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 56 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: REAL300025479036 none CN(CC1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 12, 12, 12, 12, 1] 13 rigid atoms, others: [46, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 29 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: REAL300025479036 none CN(CC1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 4, 7, 9, 9, 11, 11, 13, 13, 13, 13, 13, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 1, 1, 5, 5, 4, 4, 11, 11, 13] 13 rigid atoms, others: [38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479036 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479036 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479036/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479036 Building REAL300025479037 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479037' /scratch/stefan/7787258/working/building/REAL300025479037 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479037 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479037/0 /scratch/stefan/7787258/working/building/REAL300025479037 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/938 `/scratch/stefan/7787258/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C) `REAL300025479037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479037 none CC[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 4, 6, 6, 10, 10, 19, 29, 75, 75, 75, 75, 75, 1, 6, 8, 8, 8, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 19, 19, 75, 1, 1, 8, 8, 8, 8, 8, 8] 82 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479037 none CC[C@@H](C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 75, 82, 75, 75, 75, 62, 59, 49, 59, 32, 49, 13, 1, 1, 1, 1, 1, 1, 1, 75, 82, 82, 82, 82, 82, 82, 82, 82, 82, 75, 75, 75, 75, 75, 62, 62, 59, 59, 59, 32, 32, 1, 75, 75, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 297 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479037 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479037 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479037/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479037 Building REAL300025479038 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479038' /scratch/stefan/7787258/working/building/REAL300025479038 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479038 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479038/0 /scratch/stefan/7787258/working/building/REAL300025479038 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/939 `/scratch/stefan/7787258/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(F)F) `REAL300025479038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479038 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 23, 23, 51, 81, 172, 172, 172, 172, 172, 1, 7, 6, 8, 8, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 51, 51, 172, 1, 1, 8, 8, 8] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 44, 34, 21, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 433 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479038 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 188, 172, 188, 172, 172, 172, 159, 111, 71, 111, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 172, 199, 190, 201, 201, 199, 199, 199, 199, 172, 172, 172, 172, 172, 159, 159, 111, 111, 111, 30, 30, 1, 172, 172, 201, 201, 201] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 861 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479038 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479038 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479038/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479038 Building REAL300025479039 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479039' /scratch/stefan/7787258/working/building/REAL300025479039 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479039 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479039/0 /scratch/stefan/7787258/working/building/REAL300025479039 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/940 `/scratch/stefan/7787258/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1) `REAL300025479039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479039 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 31, 41, 41, 49, 49, 75, 116, 201, 201, 201, 201, 201, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 31, 31, 41, 41, 41, 75, 75, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 48, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 547 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479039 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 150, 166, 150, 150, 150, 127, 95, 65, 95, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 127, 127, 95, 95, 95, 29, 29, 1, 150, 150, 201] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 695 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479039 none CC1=NC(C)=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 19, 19, 41, 65, 150, 150, 150, 150, 150, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 41, 41, 150, 1, 1, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 357 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479039 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479039 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479039/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479039 Building REAL300025479040 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479040' /scratch/stefan/7787258/working/building/REAL300025479040 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479040 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479040/0 /scratch/stefan/7787258/working/building/REAL300025479040 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/941 `/scratch/stefan/7787258/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1) `REAL300025479040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479040 none CC1=NN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 9, 9, 12, 12, 12, 12, 34, 46, 46, 55, 55, 80, 122, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 6, 6, 12, 12, 12, 12, 12, 34, 34, 46, 46, 46, 80, 80, 201, 12, 12, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 48, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 574 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: REAL300025479040 none CC1=NN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 153, 116, 153, 116, 116, 116, 100, 74, 56, 74, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 200, 200, 116, 116, 116, 116, 116, 100, 100, 74, 74, 74, 29, 29, 1, 116, 116, 201, 201] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 843 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: REAL300025479040 none CC1=NN(CC(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 16, 16, 32, 49, 116, 116, 116, 116, 116, 1, 12, 12, 12, 12, 12, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 116, 1, 1, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 45, 46, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 296 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479040 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479040 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479040/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479040 Building REAL300025479041 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479041' /scratch/stefan/7787258/working/building/REAL300025479041 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479041 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479041/0 /scratch/stefan/7787258/working/building/REAL300025479041 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/942 `/scratch/stefan/7787258/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=NNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=NNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 23, 41, 41, 41, 41, 1, 8, 11, 11, 16, 16, 39, 39, 39, 39, 39, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 23, 23, 41, 41, 1, 1, 16, 16, 39] 139 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 213 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: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=NNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [32, 31, 32, 34, 39, 39, 39, 39, 47, 47, 116, 126, 139, 139, 139, 139, 39, 28, 31, 12, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 34, 34, 39, 39, 39, 39, 39, 116, 116, 126, 126, 139, 139, 39, 39, 28, 28, 1] 139 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 548 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: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=NNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [81, 61, 41, 41, 41, 41, 27, 11, 27, 7, 1, 1, 1, 1, 1, 1, 41, 81, 98, 98, 105, 105, 139, 139, 139, 139, 139, 81, 81, 81, 61, 61, 41, 41, 41, 41, 41, 11, 11, 7, 7, 1, 1, 41, 41, 105, 105, 139] 139 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 455 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479041 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479041/1 /scratch/stefan/7787258/working/building/REAL300025479041 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/943 `/scratch/stefan/7787258/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=CNN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479041.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=CNN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 26, 58, 58, 58, 58, 1, 8, 12, 12, 16, 16, 38, 38, 38, 38, 38, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 26, 26, 58, 58, 1, 1, 16, 16, 38] 169 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 245 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: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=CNN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [33, 31, 33, 34, 38, 38, 38, 38, 56, 56, 139, 151, 169, 169, 169, 169, 38, 28, 31, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 34, 34, 38, 38, 38, 38, 38, 139, 139, 151, 151, 169, 169, 38, 38, 28, 28, 1] 169 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 652 number of broken/clashed sets: 98 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479041 none CN(CC1CCN(C(=O)CCC2=CNN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [106, 81, 58, 58, 58, 58, 40, 15, 40, 8, 1, 1, 1, 1, 1, 1, 58, 106, 130, 130, 137, 137, 169, 169, 169, 169, 169, 106, 106, 106, 81, 81, 58, 58, 58, 58, 58, 15, 15, 8, 8, 1, 1, 58, 58, 137, 137, 169] 169 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 557 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479041 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479041 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479041/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479041/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479041 Building REAL300025479042 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479042' /scratch/stefan/7787258/working/building/REAL300025479042 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479042 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479042/0 /scratch/stefan/7787258/working/building/REAL300025479042 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/944 `/scratch/stefan/7787258/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(CF)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479042 none CN(CC1CCN(C(=O)C2(CF)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 4, 4, 4, 1, 7, 9, 9, 10, 10, 18, 18, 18, 18, 18, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 6, 6, 4, 4, 4, 4, 4, 4, 1, 1, 10, 10, 18] 21 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 68 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479042 none CN(CC1CCN(C(=O)C2(CF)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 15, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 18, 14, 14, 10, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 15, 15, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 14, 14, 1] 21 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479042 none CN(CC1CCN(C(=O)C2(CF)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 7, 4, 4, 4, 4, 2, 1, 2, 1, 1, 6, 1, 1, 1, 4, 11, 14, 14, 15, 15, 21, 21, 21, 21, 21, 11, 11, 11, 7, 7, 4, 4, 4, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 21] 21 rigid atoms, others: [43, 38, 7, 40, 9, 10, 39, 12, 13, 14, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48]) total number of confs: 82 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479042 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479042 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479042/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479042 Building REAL300025479043 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479043' /scratch/stefan/7787258/working/building/REAL300025479043 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479043 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479043/0 /scratch/stefan/7787258/working/building/REAL300025479043 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/945 `/scratch/stefan/7787258/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479043 none C=C[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 17, 22, 22, 25, 25, 59, 90, 201, 201, 201, 201, 201, 7, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 22, 22, 22, 59, 59, 201, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 498 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479043 none C=C[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 169, 201, 150, 169, 150, 150, 150, 122, 77, 52, 77, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 122, 122, 77, 77, 77, 30, 30, 1, 150, 150] 201 rigid atoms, others: [48, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 776 number of broken/clashed sets: 133 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479043 none C=C[C@@H]1OCC[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 7, 7, 7, 2, 7, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 25, 40, 150, 150, 150, 150, 150, 1, 18, 18, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 25, 25, 150, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 49, 50, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 328 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479043 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479043 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479043/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479043 Building REAL300025479044 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479044' /scratch/stefan/7787258/working/building/REAL300025479044 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479044 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479044/0 /scratch/stefan/7787258/working/building/REAL300025479044 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/946 `/scratch/stefan/7787258/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479044 none CC(C)C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 21, 30, 30, 30, 30, 53, 82, 171, 171, 171, 171, 171, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 10, 10, 10, 10, 10, 21, 21, 30, 30, 30, 53, 53, 171, 10, 10] 201 rigid atoms, others: [3, 4, 5, 38, 7, 8, 9, 39, 6] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 439 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479044 none CC(C)C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 171, 171, 171, 100, 171, 93, 100, 93, 93, 93, 81, 58, 42, 58, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 93, 93, 93, 93, 93, 81, 81, 58, 58, 58, 28, 28, 1, 93, 93] 201 rigid atoms, others: [52, 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, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 820 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: REAL300025479044 none CC(C)C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 2, 10, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 19, 30, 93, 93, 93, 93, 93, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 19, 19, 93, 1, 1] 201 rigid atoms, others: [43, 40, 9, 42, 11, 12, 13, 14, 15, 53, 54, 41, 28, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 246 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479044 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479044 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479044/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479044 Building REAL300025479045 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479045' /scratch/stefan/7787258/working/building/REAL300025479045 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479045 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479045/0 /scratch/stefan/7787258/working/building/REAL300025479045 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/947 `/scratch/stefan/7787258/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479045 none CC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 25, 32, 32, 32, 32, 58, 90, 201, 201, 201, 201, 201, 11, 3, 3, 3, 3, 3, 1, 1, 11, 11, 11, 11, 11, 25, 25, 32, 32, 32, 58, 58, 201, 11, 11] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 470 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479045 none CC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 127, 201, 115, 127, 115, 115, 115, 100, 71, 52, 71, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 115, 100, 100, 71, 71, 71, 30, 30, 1, 115, 115] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 782 number of broken/clashed sets: 99 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479045 none CC[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 2, 11, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 22, 36, 115, 115, 115, 115, 115, 1, 19, 19, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 22, 22, 115, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 291 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479045 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479045 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479045/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479045 Building REAL300025479046 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479046' /scratch/stefan/7787258/working/building/REAL300025479046 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479046 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479046/0 /scratch/stefan/7787258/working/building/REAL300025479046 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/948 `/scratch/stefan/7787258/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479046 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 14, 30, 30, 59, 81, 155, 155, 155, 155, 155, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 59, 59, 155] 201 rigid atoms, others: [3, 2, 35, 4, 5, 6, 39, 7, 46, 47, 19, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 48, 49, 50]) total number of confs: 402 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479046 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 83, 97, 134, 155, 155, 155, 155, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 37, 83, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 134, 134, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 155, 155, 37, 37, 1] 201 rigid atoms, others: [50, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 799 number of broken/clashed sets: 75 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479046 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 30, 59, 59, 101, 130, 201, 201, 201, 201, 201, 30, 30, 30, 20, 20, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 101, 101, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49, 50]) total number of confs: 587 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479046 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479046 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479046/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479046 Building REAL300025479047 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479047' /scratch/stefan/7787258/working/building/REAL300025479047 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479047 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479047/0 /scratch/stefan/7787258/working/building/REAL300025479047 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/949 `/scratch/stefan/7787258/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(C)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479047 none CCC(NC(C)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 3, 6, 14, 14, 14, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 21, 35, 127, 127, 127, 127, 127, 1, 11, 11, 11, 11, 11, 6, 14, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 21, 21, 127, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 50, 51, 41, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 309 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479047 none CCC(NC(C)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 187, 137, 187, 201, 201, 201, 127, 137, 127, 127, 127, 119, 81, 53, 81, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 127, 201, 201, 201, 201, 201, 187, 201, 201, 201, 201, 127, 127, 127, 127, 127, 119, 119, 81, 81, 81, 30, 30, 1, 127, 127] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 996 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479047 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479047 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479047/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479047 Building REAL300025479048 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479048' /scratch/stefan/7787258/working/building/REAL300025479048 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479048 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479048/0 /scratch/stefan/7787258/working/building/REAL300025479048 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/950 `/scratch/stefan/7787258/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479048 none CC(C)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 15, 14, 12, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 10, 10, 22, 37, 105, 105, 105, 105, 105, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 22, 22, 105, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 271 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479048 none CC(C)CCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 116, 105, 116, 105, 105, 105, 94, 69, 50, 69, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 105, 105, 105, 105, 105, 94, 94, 69, 69, 69, 30, 30, 1, 105, 105] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 875 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479048 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479048 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479048/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479048 Building REAL300025479049 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479049' /scratch/stefan/7787258/working/building/REAL300025479049 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479049 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479049/0 /scratch/stefan/7787258/working/building/REAL300025479049 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/951 `/scratch/stefan/7787258/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479049 none CN(CC1CCN(C(=O)CN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 19, 33, 33, 33, 33, 1, 10, 15, 15, 24, 25, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 19, 19, 33, 33, 1, 1, 24, 24, 50] 118 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479049 none CN(CC1CCN(C(=O)CN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [42, 40, 42, 47, 50, 50, 50, 50, 72, 72, 112, 118, 118, 118, 118, 50, 29, 40, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 47, 47, 50, 50, 50, 50, 50, 112, 112, 118, 118, 50, 50, 29, 29, 1] 118 rigid atoms, others: [44, 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]) total number of confs: 473 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479049 none CN(CC1CCN(C(=O)CN2C=NC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [64, 47, 33, 33, 33, 33, 20, 8, 20, 1, 1, 1, 1, 1, 1, 33, 64, 76, 76, 92, 92, 118, 118, 118, 118, 118, 64, 64, 64, 47, 47, 33, 33, 33, 33, 33, 8, 8, 1, 1, 33, 33, 92, 92, 118] 118 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 392 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479049 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479049 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479049/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479049 Building REAL300025479050 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479050' /scratch/stefan/7787258/working/building/REAL300025479050 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479050 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479050/0 /scratch/stefan/7787258/working/building/REAL300025479050 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/952 `/scratch/stefan/7787258/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCNC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479050 none CN(CC1CCN(C(=O)CCNC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 16, 31, 48, 48, 48, 1, 8, 10, 10, 14, 14, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 31, 31, 48, 48, 48, 1, 1, 14, 14, 43] 125 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479050 none CN(CC1CCN(C(=O)CCNC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 39, 43, 43, 43, 43, 60, 60, 108, 119, 125, 125, 125, 43, 29, 36, 12, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 39, 39, 43, 43, 43, 43, 43, 108, 108, 119, 119, 125, 125, 125, 43, 43, 29, 29, 1] 125 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 529 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479050 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479050 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479050/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479050 Building REAL300025479051 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479051' /scratch/stefan/7787258/working/building/REAL300025479051 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479051 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479051/0 /scratch/stefan/7787258/working/building/REAL300025479051 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/953 `/scratch/stefan/7787258/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479051 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 23, 37, 37, 54, 54, 83, 126, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 37, 37, 37, 83, 83, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 568 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479051 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 135, 116, 135, 116, 116, 116, 99, 78, 58, 78, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 116, 99, 99, 78, 78, 78, 29, 29, 1, 116, 116] 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, 46, 47]) total number of confs: 638 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479051 none CC1=CN=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 5, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 34, 53, 116, 116, 116, 116, 116, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 34, 34, 116, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 7, 9, 10, 11, 12, 13, 46, 47, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479051 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479051 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479051/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479051 Building REAL300025479052 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479052' /scratch/stefan/7787258/working/building/REAL300025479052 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479052 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479052/0 /scratch/stefan/7787258/working/building/REAL300025479052 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/954 `/scratch/stefan/7787258/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479052 none CN(CC1CCN(C(=O)C2CCC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 15, 36, 36, 75, 99, 173, 173, 173, 173, 173, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 75, 75, 173] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 471 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479052 none CN(CC1CCN(C(=O)C2CCC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 84, 103, 151, 173, 173, 173, 173, 186, 186, 201, 201, 201, 201, 201, 173, 39, 84, 13, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 151, 151, 173, 173, 173, 173, 173, 201, 201, 201, 201, 201, 173, 173, 39, 39, 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: 804 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479052 none CN(CC1CCN(C(=O)C2CCC2(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 39, 73, 73, 114, 142, 201, 201, 201, 201, 201, 39, 39, 39, 21, 21, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 114, 114, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 598 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479052 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479052 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479052/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479052 Building REAL300025479053 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479053' /scratch/stefan/7787258/working/building/REAL300025479053 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479053 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479053/0 /scratch/stefan/7787258/working/building/REAL300025479053 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/955 `/scratch/stefan/7787258/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479053 none CN(CC1CCN(C(=O)C2=NSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 1, 12, 29, 29, 50, 74, 135, 135, 135, 135, 135, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 50, 50, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 350 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: REAL300025479053 none CN(CC1CCN(C(=O)C2=NSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 58, 67, 114, 135, 135, 135, 135, 197, 197, 201, 201, 201, 201, 135, 34, 58, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 114, 114, 135, 135, 135, 135, 135, 201, 201, 135, 135, 34, 34, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 822 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: REAL300025479053 none CN(CC1CCN(C(=O)C2=NSC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 8, 38, 65, 65, 104, 134, 201, 201, 201, 201, 201, 38, 38, 38, 22, 22, 8, 8, 8, 8, 8, 1, 1, 8, 8, 104, 104, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 589 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479053 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479053 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479053/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479053 Building REAL300025479054 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479054' /scratch/stefan/7787258/working/building/REAL300025479054 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479054 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479054/0 /scratch/stefan/7787258/working/building/REAL300025479054 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/956 `/scratch/stefan/7787258/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1) `REAL300025479054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479054 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 50, 85, 187, 187, 187, 187, 187, 1, 5, 6, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 50, 50, 187, 1, 1, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 44, 34, 21, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 439 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479054 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 4, 4, 6, 6, 6, 6, 18, 29, 29, 43, 43, 81, 122, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 3, 3, 3, 2, 6, 6, 6, 6, 6, 18, 18, 29, 29, 29, 81, 81, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 45, 46, 47, 48, 49, 50, 51, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 574 number of broken/clashed sets: 57 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479054 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 201, 187, 187, 187, 167, 104, 66, 104, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 187, 187, 167, 167, 104, 104, 104, 30, 30, 1, 187, 187, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 760 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479054 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479054 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479054/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479054 Building REAL300025479055 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479055' /scratch/stefan/7787258/working/building/REAL300025479055 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479055 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479055/0 /scratch/stefan/7787258/working/building/REAL300025479055 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/957 `/scratch/stefan/7787258/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2C=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479055 none CN(CC1CCN(C(=O)CC2C=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 32, 32, 32, 32, 32, 1, 8, 12, 12, 17, 17, 44, 44, 44, 44, 44, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 17, 17, 44] 132 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 213 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: REAL300025479055 none CN(CC1CCN(C(=O)CC2C=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [36, 34, 36, 39, 44, 44, 44, 44, 53, 53, 125, 132, 132, 132, 132, 132, 44, 29, 34, 13, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 39, 39, 44, 44, 44, 44, 44, 125, 125, 132, 132, 132, 132, 132, 132, 132, 132, 132, 44, 44, 29, 29, 1] 132 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 538 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: REAL300025479055 none CN(CC1CCN(C(=O)CC2C=CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [72, 55, 32, 32, 32, 32, 16, 5, 16, 1, 1, 1, 1, 1, 1, 1, 32, 72, 90, 90, 97, 97, 132, 132, 132, 132, 132, 72, 72, 72, 55, 55, 32, 32, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 97, 97, 132] 132 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 422 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479055 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479055 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479055/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479055 Building REAL300025479056 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479056' /scratch/stefan/7787258/working/building/REAL300025479056 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479056 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479056/0 /scratch/stefan/7787258/working/building/REAL300025479056 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/958 `/scratch/stefan/7787258/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025479056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479056 none CCOCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 9, 14, 14, 18, 18, 37, 59, 162, 162, 162, 162, 162, 3, 1, 1, 14, 14, 14, 14, 14, 6, 6, 3, 3, 3, 3, 3, 9, 9, 14, 14, 14, 37, 37, 162, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 49, 50, 51, 52, 25, 26] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 376 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479056 none CCOCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 162, 162, 151, 162, 151, 151, 151, 126, 93, 62, 93, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 151, 162, 162, 201, 201, 201, 201, 201, 200, 200, 151, 151, 151, 151, 151, 126, 126, 93, 93, 93, 30, 30, 1, 151, 151, 162, 162, 162, 162] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 827 number of broken/clashed sets: 117 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479056 none CCOCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 15, 15, 33, 53, 151, 151, 151, 151, 151, 1, 3, 3, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 33, 33, 151, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 353 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479056 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479056 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479056/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479056 Building REAL300025479057 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479057' /scratch/stefan/7787258/working/building/REAL300025479057 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479057 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479057/0 /scratch/stefan/7787258/working/building/REAL300025479057 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/959 `/scratch/stefan/7787258/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC3C=CC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479057 none CN(CC1CCN(C(=O)C2CC3C=CC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 1, 14, 33, 33, 62, 84, 157, 157, 157, 157, 157, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 62, 62, 157] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 424 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479057 none CN(CC1CCN(C(=O)C2CC3C=CC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 80, 91, 136, 157, 157, 157, 157, 160, 160, 201, 201, 201, 201, 201, 201, 157, 36, 80, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 136, 136, 157, 157, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 157, 157, 36, 36, 1] 201 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 809 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: REAL300025479057 none CN(CC1CCN(C(=O)C2CC3C=CC2O3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 29, 60, 60, 103, 133, 201, 201, 201, 201, 201, 29, 29, 29, 20, 20, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 103, 103, 201] 201 rigid atoms, others: [43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48]) total number of confs: 600 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479057 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479057 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479057/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479057 Building REAL300025479058 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479058' /scratch/stefan/7787258/working/building/REAL300025479058 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479058 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479058/0 /scratch/stefan/7787258/working/building/REAL300025479058 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/960 `/scratch/stefan/7787258/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479058 none COC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 21, 27, 27, 37, 37, 65, 101, 201, 201, 201, 201, 201, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 21, 21, 27, 27, 27, 65, 65, 201, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 37, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 496 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479058 none COC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 159, 134, 159, 134, 134, 134, 118, 84, 59, 84, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 118, 118, 84, 84, 84, 30, 30, 1, 134, 134] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 783 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479058 none COC1CCCC1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 35, 58, 134, 134, 134, 134, 134, 1, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 35, 35, 134, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 318 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479058 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479058 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479058/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479058 Building REAL300025479059 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479059' /scratch/stefan/7787258/working/building/REAL300025479059 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479059 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479059/0 /scratch/stefan/7787258/working/building/REAL300025479059 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/961 `/scratch/stefan/7787258/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CO1) `REAL300025479059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479059 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 21, 31, 31, 45, 45, 75, 120, 201, 201, 201, 201, 201, 8, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 31, 31, 31, 75, 75, 201, 8, 8, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 48, 49, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 545 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: REAL300025479059 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 134, 150, 134, 134, 134, 120, 87, 58, 87, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 120, 120, 87, 87, 87, 28, 28, 1, 134, 134, 201, 201] 201 rigid atoms, others: [45, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 775 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: REAL300025479059 none CC1CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 37, 63, 134, 134, 134, 134, 134, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 37, 37, 134, 1, 1, 8, 8] 201 rigid atoms, others: [33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 46, 47, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 328 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479059 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479059 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479059/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479059 Building REAL300025479060 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479060' /scratch/stefan/7787258/working/building/REAL300025479060 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479060 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479060/0 /scratch/stefan/7787258/working/building/REAL300025479060 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/962 `/scratch/stefan/7787258/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479060 none CN(CC1CCN(C(=O)C2CCCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 14, 33, 33, 71, 96, 163, 163, 163, 163, 163, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 71, 71, 163] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 453 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: REAL300025479060 none CN(CC1CCN(C(=O)C2CCCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 95, 141, 163, 163, 163, 163, 182, 182, 201, 201, 201, 201, 201, 201, 163, 38, 72, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 141, 141, 163, 163, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 38, 38, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 820 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: REAL300025479060 none CN(CC1CCN(C(=O)C2CCCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 30, 58, 58, 107, 138, 201, 201, 201, 201, 201, 30, 30, 30, 16, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 107, 107, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 601 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479060 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479060 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479060/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479060 Building REAL300025479061 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479061' /scratch/stefan/7787258/working/building/REAL300025479061 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479061 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479061/0 /scratch/stefan/7787258/working/building/REAL300025479061 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/963 `/scratch/stefan/7787258/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479061 none CN(CC1CCN(C(=O)CC2CCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 19, 34, 34, 34, 34, 34, 1, 8, 12, 12, 17, 18, 48, 48, 48, 48, 48, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 17, 17, 48] 147 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479061 none CN(CC1CCN(C(=O)CC2CCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [40, 38, 40, 43, 48, 48, 48, 48, 60, 60, 139, 147, 147, 147, 147, 147, 48, 32, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 43, 43, 48, 48, 48, 48, 48, 139, 139, 147, 147, 147, 147, 147, 147, 147, 147, 147, 48, 48, 32, 32, 1] 147 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 597 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479061 none CN(CC1CCN(C(=O)CC2CCC3CC32)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [79, 57, 34, 34, 34, 34, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 34, 79, 102, 102, 115, 115, 147, 147, 147, 147, 147, 79, 79, 79, 57, 57, 34, 34, 34, 34, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 115, 115, 147] 147 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 502 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479061 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479061 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479061/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479061 Building REAL300025479062 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479062' /scratch/stefan/7787258/working/building/REAL300025479062 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479062 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479062/0 /scratch/stefan/7787258/working/building/REAL300025479062 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/964 `/scratch/stefan/7787258/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479062 none CN(CC1CCN(C(=O)C2CCC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 12, 29, 29, 57, 75, 128, 128, 128, 128, 128, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 57, 57, 128] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 366 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479062 none CN(CC1CCN(C(=O)C2CCC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 61, 75, 110, 128, 128, 128, 128, 138, 138, 201, 201, 201, 201, 201, 201, 128, 35, 61, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 110, 110, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 35, 35, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 816 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479062 none CN(CC1CCN(C(=O)C2CCC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 30, 60, 60, 108, 138, 201, 201, 201, 201, 201, 30, 30, 30, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 108, 108, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 607 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479062 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479062 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479062/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479062 Building REAL300025479063 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479063' /scratch/stefan/7787258/working/building/REAL300025479063 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479063 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479063/0 /scratch/stefan/7787258/working/building/REAL300025479063 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/965 `/scratch/stefan/7787258/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479063 none CCC(C)C(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 3, 6, 8, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 28, 46, 116, 116, 116, 116, 116, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 8, 8, 8, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 28, 28, 116, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479063 none CCC(C)C(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 201, 135, 200, 200, 116, 135, 116, 116, 116, 101, 69, 49, 69, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 116, 116, 116, 116, 116, 101, 101, 69, 69, 69, 27, 27, 1, 116, 116] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 922 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479063 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479063 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479063/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479063 Building REAL300025479064 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479064' /scratch/stefan/7787258/working/building/REAL300025479064 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479064 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479064/0 /scratch/stefan/7787258/working/building/REAL300025479064 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/966 `/scratch/stefan/7787258/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1) `REAL300025479064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479064 none COC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 17, 25, 25, 25, 25, 54, 87, 201, 201, 201, 201, 201, 7, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 25, 25, 25, 54, 54, 201, 7, 7, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 52, 26, 51, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 469 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479064 none COC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 129, 120, 129, 120, 120, 120, 100, 69, 49, 69, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 120, 120, 100, 100, 69, 69, 69, 29, 29, 1, 120, 120, 201, 201] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 764 number of broken/clashed sets: 112 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479064 none COC1CCC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 10, 10, 23, 39, 120, 120, 120, 120, 120, 1, 7, 14, 14, 14, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 120, 1, 1, 7, 7] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 25, 49, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 265 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479064 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479064 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479064/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479064 Building REAL300025479065 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479065' /scratch/stefan/7787258/working/building/REAL300025479065 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479065 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479065/0 /scratch/stefan/7787258/working/building/REAL300025479065 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/967 `/scratch/stefan/7787258/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479065 none CCC(CC)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 7, 8, 10, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 14, 14, 30, 50, 131, 131, 131, 131, 131, 1, 10, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 30, 30, 131, 1, 1] 201 rigid atoms, others: [43, 7, 9, 42, 11, 12, 45, 46, 44, 13, 55, 56, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 330 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479065 none CCC(CC)C(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 183, 201, 144, 183, 131, 144, 131, 131, 131, 117, 83, 57, 83, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 183, 201, 201, 201, 201, 201, 183, 183, 183, 183, 131, 131, 131, 131, 131, 117, 117, 83, 83, 83, 29, 29, 1, 131, 131] 201 rigid atoms, others: [54, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56]) total number of confs: 1000 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479065 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479065 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479065/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479065 Building REAL300025479066 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479066' /scratch/stefan/7787258/working/building/REAL300025479066 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479066 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479066/0 /scratch/stefan/7787258/working/building/REAL300025479066 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/968 `/scratch/stefan/7787258/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC23CC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479066 none CN(CC1CCN(C(=O)C2CC23CC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 1, 14, 31, 31, 58, 79, 147, 147, 147, 147, 147, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 58, 58, 147] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 398 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479066 none CN(CC1CCN(C(=O)C2CC23CC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 73, 86, 127, 147, 147, 147, 147, 162, 162, 201, 201, 201, 201, 147, 37, 73, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 127, 127, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 147, 147, 37, 37, 1] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 798 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479066 none CN(CC1CCN(C(=O)C2CC23CC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 12, 39, 73, 73, 113, 139, 201, 201, 201, 201, 201, 39, 39, 39, 24, 24, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 113, 113, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) total number of confs: 610 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479066 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479066 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479066/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479066 Building REAL300025479067 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479067' /scratch/stefan/7787258/working/building/REAL300025479067 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479067 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479067/0 /scratch/stefan/7787258/working/building/REAL300025479067 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/969 `/scratch/stefan/7787258/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479067 none CN(CC1CCN(C(=O)CC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 20, 37, 37, 37, 37, 1, 10, 15, 15, 24, 25, 56, 56, 56, 56, 56, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 20, 20, 37, 37, 37, 1, 1, 24, 24, 56] 177 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 230 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479067 none CN(CC1CCN(C(=O)CC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 43, 45, 49, 56, 56, 56, 56, 77, 77, 171, 177, 177, 177, 177, 56, 32, 43, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 49, 49, 56, 56, 56, 56, 56, 171, 171, 177, 177, 177, 56, 56, 32, 32, 1] 177 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: 699 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479067 none CN(CC1CCN(C(=O)CC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 62, 37, 37, 37, 37, 23, 5, 23, 1, 1, 1, 1, 1, 1, 37, 88, 112, 112, 135, 136, 177, 177, 177, 177, 177, 88, 88, 88, 62, 62, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 37, 37, 135, 135, 177] 177 rigid atoms, others: [38, 39, 40, 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, 41, 42, 43, 44, 45]) total number of confs: 596 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479067 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479067 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479067/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479067 Building REAL300025479068 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479068' /scratch/stefan/7787258/working/building/REAL300025479068 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479068 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479068/0 /scratch/stefan/7787258/working/building/REAL300025479068 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/970 `/scratch/stefan/7787258/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479068 none C=CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 4, 8, 8, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 17, 82, 82, 82, 82, 82, 1, 30, 30, 30, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 82, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 238 number of broken/clashed sets: 193 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479068 none C=CCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 120, 175, 175, 82, 120, 82, 82, 82, 82, 58, 58, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 175, 82, 82, 82, 82, 82, 82, 82, 58, 58, 58, 30, 30, 1, 82, 82] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 916 number of broken/clashed sets: 193 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479068 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479068 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479068/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479068 Building REAL300025479069 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479069' /scratch/stefan/7787258/working/building/REAL300025479069 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479069 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479069/0 /scratch/stefan/7787258/working/building/REAL300025479069 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/971 `/scratch/stefan/7787258/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)N1) `REAL300025479069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479069 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 29, 40, 40, 53, 53, 77, 119, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 29, 29, 40, 40, 40, 77, 77, 201, 11, 11, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 49, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 549 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: REAL300025479069 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 134, 158, 134, 134, 134, 113, 82, 59, 82, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 134, 134, 134, 134, 134, 113, 113, 82, 82, 82, 30, 30, 1, 134, 134, 201, 201, 201, 201] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 677 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: REAL300025479069 none CC1=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 6, 11, 11, 20, 20, 38, 60, 134, 134, 134, 134, 134, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 38, 38, 134, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 324 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479069 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479069 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479069/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479069 Building REAL300025479070 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479070' /scratch/stefan/7787258/working/building/REAL300025479070 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479070 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479070/0 /scratch/stefan/7787258/working/building/REAL300025479070 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/972 `/scratch/stefan/7787258/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC23CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479070 none CN(CC1CCN(C(=O)C2CC23CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 1, 11, 29, 29, 58, 79, 163, 163, 163, 163, 163, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 58, 58, 163] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 34, 46, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 420 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479070 none CN(CC1CCN(C(=O)C2CC23CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 95, 143, 163, 163, 163, 163, 178, 178, 201, 201, 201, 201, 201, 163, 38, 78, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 143, 143, 163, 163, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 163, 38, 38, 1] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 803 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479070 none CN(CC1CCN(C(=O)C2CC23CCC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 25, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 37, 64, 64, 109, 136, 201, 201, 201, 201, 201, 37, 37, 37, 25, 25, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 109, 109, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 606 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479070 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479070 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479070/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479070 Building REAL300025479071 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479071' /scratch/stefan/7787258/working/building/REAL300025479071 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479071 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479071/0 /scratch/stefan/7787258/working/building/REAL300025479071 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/973 `/scratch/stefan/7787258/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479071 none CC1=CC=NN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 9, 9, 9, 9, 21, 28, 28, 48, 48, 78, 118, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 1, 4, 4, 9, 9, 9, 9, 9, 21, 21, 28, 28, 28, 78, 78, 201, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 558 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479071 none CC1=CC=NN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 148, 110, 148, 110, 110, 110, 103, 74, 48, 74, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 103, 103, 74, 74, 74, 26, 26, 1, 110, 110] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 837 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479071 none CC1=CC=NN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 8, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 19, 19, 36, 57, 110, 110, 110, 110, 110, 1, 9, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 36, 36, 110, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 302 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479071 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479071 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479071/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479071 Building REAL300025479072 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479072' /scratch/stefan/7787258/working/building/REAL300025479072 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479072 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479072/0 /scratch/stefan/7787258/working/building/REAL300025479072 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/974 `/scratch/stefan/7787258/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479072 none CC1=CNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 30, 41, 41, 54, 54, 80, 117, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 41, 41, 41, 80, 80, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 544 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479072 none CC1=CNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 162, 139, 162, 139, 139, 139, 119, 92, 64, 92, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 119, 119, 92, 92, 92, 29, 29, 1, 139, 139] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 692 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479072 none CC1=CNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 22, 22, 42, 63, 139, 139, 139, 139, 139, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 42, 42, 139, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 334 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479072 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479072 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479072/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479072 Building REAL300025479073 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479073' /scratch/stefan/7787258/working/building/REAL300025479073 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479073 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479073/0 /scratch/stefan/7787258/working/building/REAL300025479073 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/975 `/scratch/stefan/7787258/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479073 none CN(CC1CCN(C(=O)C2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 1, 12, 26, 26, 45, 70, 149, 149, 149, 149, 149, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 45, 45, 149] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 346 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: REAL300025479073 none CN(CC1CCN(C(=O)C2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 76, 87, 137, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 149, 36, 76, 13, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 137, 137, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 149, 149, 36, 36, 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: 821 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: REAL300025479073 none CN(CC1CCN(C(=O)C2=NN(C)C=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 31, 58, 58, 87, 128, 201, 201, 201, 201, 201, 31, 31, 31, 18, 18, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 7, 7, 87, 87, 201] 201 rigid atoms, others: [7, 40, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 43, 44, 45]) total number of confs: 536 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479073 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479073 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479073/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479073 Building REAL300025479074 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479074' /scratch/stefan/7787258/working/building/REAL300025479074 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479074 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479074/0 /scratch/stefan/7787258/working/building/REAL300025479074 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/976 `/scratch/stefan/7787258/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479074 none CC1=NC=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 22, 22, 22, 22, 36, 41, 41, 43, 43, 77, 111, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 5, 5, 22, 22, 22, 22, 22, 36, 36, 41, 41, 41, 77, 77, 201, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 575 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479074 none CC1=NC=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 101, 97, 101, 97, 97, 97, 77, 64, 46, 64, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 167, 167, 97, 97, 97, 97, 97, 77, 77, 64, 64, 64, 28, 28, 1, 97, 97] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 765 number of broken/clashed sets: 132 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479074 none CC1=NC=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 22, 36, 97, 97, 97, 97, 97, 1, 22, 22, 22, 22, 22, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 22, 22, 97, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 264 number of broken/clashed sets: 132 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479074 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479074/1 /scratch/stefan/7787258/working/building/REAL300025479074 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/977 `/scratch/stefan/7787258/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479074.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479074 none CC1=[NH+]C=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 16, 24, 27, 27, 27, 27, 60, 101, 194, 194, 194, 194, 194, 16, 2, 2, 2, 1, 1, 6, 6, 16, 16, 16, 16, 16, 24, 24, 27, 27, 27, 60, 60, 194, 16, 16] 194 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 481 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479074 none CC1=[NH+]C=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 194, 194, 164, 85, 85, 85, 85, 85, 85, 56, 51, 51, 51, 32, 51, 13, 1, 1, 1, 1, 1, 1, 1, 85, 194, 194, 194, 194, 194, 164, 164, 85, 85, 85, 85, 85, 56, 56, 51, 51, 51, 32, 32, 1, 85, 85] 194 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 739 number of broken/clashed sets: 167 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479074 none CC1=[NH+]C=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 2, 1, 2, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 12, 20, 85, 85, 85, 85, 85, 1, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 12, 12, 85, 1, 1] 194 rigid atoms, others: [35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 167 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479074 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479074 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479074/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479074/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479074 Building REAL300025479075 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479075' /scratch/stefan/7787258/working/building/REAL300025479075 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479075 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479075/0 /scratch/stefan/7787258/working/building/REAL300025479075 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/978 `/scratch/stefan/7787258/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479075 none CCN1C=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 15, 21, 21, 25, 25, 46, 67, 122, 122, 122, 122, 122, 6, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 21, 21, 21, 46, 46, 122, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 334 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479075 none CCN1C=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 122, 122, 122, 122, 122, 101, 79, 101, 79, 79, 79, 72, 59, 43, 59, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 122, 122, 122, 79, 79, 79, 79, 79, 72, 72, 59, 59, 59, 26, 26, 1, 79, 79] 201 rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 880 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479075 none CCN1C=CC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 27, 40, 79, 79, 79, 79, 79, 1, 10, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 27, 27, 79, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 48, 49, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 235 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479075 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479075 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479075/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479075 Building REAL300025479076 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479076' /scratch/stefan/7787258/working/building/REAL300025479076 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479076 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479076/0 /scratch/stefan/7787258/working/building/REAL300025479076 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/979 `/scratch/stefan/7787258/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479076 none CN(CC1CCN(C(=O)CC2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 28, 28, 28, 28, 28, 1, 8, 10, 10, 13, 13, 32, 32, 32, 32, 32, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 13, 13, 32] 87 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479076 none CN(CC1CCN(C(=O)CC2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 25, 28, 32, 32, 32, 32, 38, 38, 78, 87, 87, 87, 87, 87, 32, 23, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 28, 28, 32, 32, 32, 32, 32, 78, 78, 87, 87, 87, 87, 87, 87, 87, 87, 87, 32, 32, 23, 23, 1] 87 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 344 number of broken/clashed sets: 59 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479076 none CN(CC1CCN(C(=O)CC2CCCOC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 40, 28, 28, 28, 28, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 28, 52, 60, 60, 69, 69, 87, 87, 87, 87, 87, 52, 52, 52, 40, 40, 28, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 69, 69, 87] 87 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 293 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479076 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479076 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479076/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479076 Building REAL300025479077 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479077' /scratch/stefan/7787258/working/building/REAL300025479077 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479077 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479077/0 /scratch/stefan/7787258/working/building/REAL300025479077 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/980 `/scratch/stefan/7787258/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479077 none CN(CC1CCN(C(=O)C2CCC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 1, 13, 31, 31, 59, 79, 128, 128, 128, 128, 128, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 59, 59, 128] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 362 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: REAL300025479077 none CN(CC1CCN(C(=O)C2CCC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 66, 82, 112, 128, 128, 128, 128, 134, 134, 201, 201, 201, 201, 201, 201, 128, 36, 66, 13, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 112, 112, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 36, 36, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 807 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: REAL300025479077 none CN(CC1CCN(C(=O)C2CCC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 29, 62, 62, 106, 140, 201, 201, 201, 201, 201, 29, 29, 29, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 106, 106, 201] 201 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48, 49, 50, 51, 52]) total number of confs: 601 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479077 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479077 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479077/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479077 Building REAL300025479078 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479078' /scratch/stefan/7787258/working/building/REAL300025479078 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479078 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479078/0 /scratch/stefan/7787258/working/building/REAL300025479078 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/981 `/scratch/stefan/7787258/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1) `REAL300025479078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479078 none CC1=NC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 20, 28, 28, 51, 51, 84, 122, 201, 201, 201, 201, 201, 7, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 20, 20, 28, 28, 28, 84, 84, 201, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 571 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479078 none CC1=NC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 191, 155, 191, 155, 155, 155, 143, 94, 60, 94, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 155, 143, 143, 94, 94, 94, 29, 29, 1, 155, 155] 201 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 731 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479078 none CC1=NC=CC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 6, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 22, 22, 44, 71, 155, 155, 155, 155, 155, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 44, 44, 155, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 45, 46, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 374 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479078 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479078 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479078/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479078 Building REAL300025479079 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479079' /scratch/stefan/7787258/working/building/REAL300025479079 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479079 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479079/0 /scratch/stefan/7787258/working/building/REAL300025479079 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/982 `/scratch/stefan/7787258/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(F)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479079 none CN(CC1CCN(C(=O)C2(F)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1, 14, 33, 33, 65, 90, 142, 142, 142, 142, 142, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 65, 65, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 404 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479079 none CN(CC1CCN(C(=O)C2(F)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 81, 123, 142, 142, 142, 142, 183, 183, 201, 201, 201, 201, 201, 142, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 123, 123, 142, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 31, 31, 1] 201 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 807 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479079 none CN(CC1CCN(C(=O)C2(F)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 32, 60, 60, 110, 144, 201, 201, 201, 201, 201, 32, 32, 32, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 110, 110, 201] 201 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48]) total number of confs: 607 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479079 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479079 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479079/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479079 Building REAL300025479080 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479080' /scratch/stefan/7787258/working/building/REAL300025479080 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479080 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479080/0 /scratch/stefan/7787258/working/building/REAL300025479080 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/983 `/scratch/stefan/7787258/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479080 none CN(CC1CCN(C(=O)C2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 14, 30, 30, 51, 69, 130, 130, 130, 130, 130, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 51, 51, 130] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479080 none CN(CC1CCN(C(=O)C2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 81, 116, 130, 130, 130, 130, 178, 178, 201, 201, 201, 201, 201, 130, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 116, 116, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 130, 130, 37, 37, 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: 760 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479080 none CN(CC1CCN(C(=O)C2=CN=CN2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 23, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 44, 70, 70, 109, 143, 201, 201, 201, 201, 201, 44, 44, 44, 23, 23, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 9, 9, 109, 109, 201] 201 rigid atoms, others: [36, 37, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 599 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479080 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479080 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479080/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479080 Building REAL300025479081 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479081' /scratch/stefan/7787258/working/building/REAL300025479081 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479081 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479081/0 /scratch/stefan/7787258/working/building/REAL300025479081 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/984 `/scratch/stefan/7787258/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1) `REAL300025479081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479081 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 15, 19, 19, 21, 21, 42, 60, 124, 124, 124, 124, 124, 8, 1, 1, 1, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 15, 15, 19, 19, 19, 42, 42, 124, 8, 8, 1] 201 rigid atoms, others: [1, 2, 3, 4, 47, 24, 25, 26] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 334 number of broken/clashed sets: 155 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479081 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 88, 64, 88, 64, 64, 64, 53, 29, 25, 29, 19, 25, 10, 1, 1, 1, 1, 1, 1, 1, 64, 124, 124, 124, 201, 201, 201, 201, 201, 64, 64, 64, 64, 64, 53, 53, 29, 29, 29, 19, 19, 1, 64, 64, 124] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 878 number of broken/clashed sets: 155 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479081 none CCC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 8, 3, 1, 3, 1, 1, 1, 1, 1, 5, 7, 7, 8, 8, 17, 26, 64, 64, 64, 64, 64, 1, 8, 8, 8, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 17, 17, 64, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47]) total number of confs: 203 number of broken/clashed sets: 155 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479081 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479081 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479081/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479081 Building REAL300025479082 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479082' /scratch/stefan/7787258/working/building/REAL300025479082 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479082 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479082/0 /scratch/stefan/7787258/working/building/REAL300025479082 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/985 `/scratch/stefan/7787258/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479082 none CN(CC1CCN(C(=O)CC2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 6, 6, 21, 27, 27, 27, 27, 1, 8, 14, 14, 21, 22, 47, 47, 47, 47, 47, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 21, 21, 27, 27, 1, 1, 21, 21, 47] 107 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 195 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: REAL300025479082 none CN(CC1CCN(C(=O)CC2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [38, 37, 38, 43, 47, 47, 47, 47, 68, 68, 99, 107, 107, 107, 107, 47, 30, 37, 12, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 43, 43, 47, 47, 47, 47, 47, 99, 99, 107, 107, 47, 47, 30, 30, 1] 107 rigid atoms, others: [44, 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]) total number of confs: 438 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: REAL300025479082 none CN(CC1CCN(C(=O)CC2=CSC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [54, 42, 27, 27, 27, 27, 14, 5, 14, 1, 1, 1, 1, 1, 1, 27, 54, 64, 64, 75, 75, 107, 107, 107, 107, 107, 54, 54, 54, 42, 42, 27, 27, 27, 27, 27, 5, 5, 1, 1, 27, 27, 75, 75, 107] 107 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43, 44]) total number of confs: 320 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479082 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479082 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479082/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479082 Building REAL300025479083 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479083' /scratch/stefan/7787258/working/building/REAL300025479083 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479083 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479083/0 /scratch/stefan/7787258/working/building/REAL300025479083 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/986 `/scratch/stefan/7787258/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479083 none CN(C)C(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 10, 10, 26, 45, 132, 132, 132, 132, 132, 1, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 26, 26, 132, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 313 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479083 none CN(C)C(=O)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 201, 145, 132, 145, 132, 132, 132, 118, 80, 52, 80, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 183, 183, 132, 132, 132, 132, 132, 118, 118, 80, 80, 80, 30, 30, 1, 132, 132] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 876 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479083 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479083 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479083/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479083 Building REAL300025479084 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479084' /scratch/stefan/7787258/working/building/REAL300025479084 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479084 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479084/0 /scratch/stefan/7787258/working/building/REAL300025479084 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/987 `/scratch/stefan/7787258/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479084 none CN(CC1CCN(C(=O)CCC2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 2, 2, 13, 16, 21, 21, 21, 21, 1, 8, 11, 11, 14, 14, 30, 30, 30, 30, 30, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 13, 13, 16, 16, 21, 21, 21, 1, 1, 14, 14, 30] 71 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479084 none CN(CC1CCN(C(=O)CCC2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [26, 25, 26, 27, 30, 30, 30, 30, 36, 36, 69, 71, 71, 71, 71, 71, 30, 23, 25, 13, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 27, 27, 30, 30, 30, 30, 30, 69, 69, 71, 71, 71, 71, 71, 30, 30, 23, 23, 1] 71 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 42 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479084 none CN(CC1CCN(C(=O)CCC2=CNN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [56, 43, 28, 28, 28, 28, 19, 8, 19, 4, 1, 1, 1, 1, 1, 1, 28, 56, 64, 64, 72, 72, 90, 90, 90, 90, 90, 56, 56, 56, 43, 43, 28, 28, 29, 29, 29, 8, 8, 4, 4, 1, 1, 1, 28, 28, 72, 72, 90] 90 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 317 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479084 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479084 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479084/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479084 Building REAL300025479085 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479085' /scratch/stefan/7787258/working/building/REAL300025479085 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479085 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479085/0 /scratch/stefan/7787258/working/building/REAL300025479085 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/988 `/scratch/stefan/7787258/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025479085 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 21, 21, 1, 6, 7, 7, 8, 8, 15, 15, 15, 15, 15, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 12, 12, 21, 21, 21, 21, 21, 1, 1, 8, 8, 15] 33 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479085 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 31, 31, 31, 31, 31, 33, 33, 15, 13, 14, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 33, 15, 15, 13, 13, 1] 33 rigid atoms, others: [49, 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, 19, 20, 28, 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: 21 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479085 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 21, 21, 21, 21, 16, 5, 16, 5, 5, 5, 1, 5, 1, 1, 1, 21, 30, 31, 31, 31, 31, 33, 33, 33, 33, 33, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 21, 21, 31, 31, 33] 33 rigid atoms, others: [40, 41, 42, 43, 12, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479085 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 16, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 21, 21, 23, 23, 31, 31, 31, 31, 31, 20, 20, 20, 16, 16, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 5, 5, 12, 12, 23, 23, 31] 33 rigid atoms, others: [38, 7, 9, 10, 11, 12, 13, 14, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479085 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479085 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479085/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479085 Building REAL300025479086 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479086' /scratch/stefan/7787258/working/building/REAL300025479086 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479086 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479086/0 /scratch/stefan/7787258/working/building/REAL300025479086 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/989 `/scratch/stefan/7787258/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025479086 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 4, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 16, 16, 16, 1, 5, 5, 5, 6, 6, 14, 14, 14, 14, 14, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 13, 13, 16, 16, 16, 16, 16, 16, 16, 1, 1, 6, 6, 14] 27 rigid atoms, others: [34, 3, 4, 5, 6, 7, 2, 48, 49, 18, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479086 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 14, 14, 14, 14, 14, 16, 16, 23, 23, 23, 23, 23, 27, 27, 27, 14, 13, 14, 11, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 27, 27, 27, 27, 27, 27, 27, 14, 14, 13, 13, 1] 27 rigid atoms, others: [52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 18 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479086 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 16, 16, 16, 16, 10, 4, 10, 4, 4, 4, 1, 4, 1, 1, 1, 1, 16, 20, 20, 20, 22, 22, 27, 27, 27, 27, 27, 20, 20, 20, 19, 19, 16, 16, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 16, 16, 22, 22, 27] 27 rigid atoms, others: [41, 42, 43, 12, 45, 14, 15, 16, 17, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479086 none CN(CC1CCN(C(=O)[C@@H]2C[C@H]2C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 16, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 17, 17, 17, 19, 19, 23, 23, 23, 23, 23, 17, 17, 17, 16, 16, 13, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 4, 4, 13, 13, 19, 19, 23] 27 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 7] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 76 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479086 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479086 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479086/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479086 Building REAL300025479087 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479087' /scratch/stefan/7787258/working/building/REAL300025479087 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479087 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479087/0 /scratch/stefan/7787258/working/building/REAL300025479087 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/990 `/scratch/stefan/7787258/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479087 none COCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 13, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 11, 11, 20, 20, 31, 41, 82, 82, 82, 82, 82, 1, 33, 33, 33, 22, 22, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 31, 31, 82, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 332 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479087 none COCCC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 154, 98, 154, 82, 98, 82, 82, 82, 68, 51, 37, 51, 18, 37, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 176, 176, 154, 154, 154, 154, 82, 82, 82, 82, 82, 68, 68, 51, 51, 51, 18, 18, 1, 82, 82] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 943 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479087 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479087 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479087/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479087 Building REAL300025479088 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479088' /scratch/stefan/7787258/working/building/REAL300025479088 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479088 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479088/0 /scratch/stefan/7787258/working/building/REAL300025479088 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/991 `/scratch/stefan/7787258/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479088 none CCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 7, 7, 9, 1, 3, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 20, 37, 110, 110, 110, 110, 110, 1, 9, 9, 9, 9, 9, 7, 7, 7, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 20, 20, 110, 1, 1] 201 rigid atoms, others: [43, 6, 39, 8, 9, 10, 11, 12, 40, 52, 53, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479088 none CCC(C)(CC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 166, 197, 197, 201, 110, 166, 110, 110, 110, 102, 71, 53, 71, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 197, 197, 197, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 102, 102, 71, 71, 71, 28, 28, 1, 110, 110] 201 rigid atoms, others: [51, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 860 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479088 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479088 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479088/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479088 Building REAL300025479089 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479089' /scratch/stefan/7787258/working/building/REAL300025479089 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479089 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479089/0 /scratch/stefan/7787258/working/building/REAL300025479089 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/992 `/scratch/stefan/7787258/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1) `REAL300025479089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479089 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 2, 2, 3, 3, 3, 3, 9, 16, 16, 31, 31, 60, 95, 189, 189, 189, 189, 189, 3, 1, 1, 10, 10, 10, 5, 5, 3, 3, 3, 3, 3, 9, 9, 16, 16, 16, 60, 60, 189, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 46, 47, 48, 49, 24, 25] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 487 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: REAL300025479089 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 189, 181, 189, 181, 181, 181, 165, 106, 63, 106, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 181, 189, 189, 201, 201, 201, 201, 201, 181, 181, 181, 181, 181, 165, 165, 106, 106, 106, 30, 30, 1, 181, 181, 189, 189, 189, 189] 201 rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 807 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: REAL300025479089 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 12, 12, 27, 27, 56, 91, 181, 181, 181, 181, 181, 1, 3, 3, 11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 56, 56, 181, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 44, 45, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 464 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479089 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479089 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479089/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479089 Building REAL300025479090 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479090' /scratch/stefan/7787258/working/building/REAL300025479090 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479090 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479090/0 /scratch/stefan/7787258/working/building/REAL300025479090 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/993 `/scratch/stefan/7787258/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479090 none COCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 8, 4, 8, 8, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 26, 74, 74, 74, 74, 74, 1, 27, 27, 27, 22, 22, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 74, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479090 none COCC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 104, 167, 167, 74, 104, 74, 74, 74, 74, 52, 52, 52, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 74, 74, 74, 74, 74, 74, 74, 52, 52, 52, 26, 26, 1, 74, 74] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 914 number of broken/clashed sets: 197 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479090 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479090 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479090/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479090 Building REAL300025479091 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479091' /scratch/stefan/7787258/working/building/REAL300025479091 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479091 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479091/0 /scratch/stefan/7787258/working/building/REAL300025479091 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/994 `/scratch/stefan/7787258/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479091 none CN(CC1CCN(C(=O)CCC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 27, 44, 44, 44, 44, 1, 9, 14, 14, 21, 21, 54, 54, 54, 54, 54, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 17, 17, 27, 27, 44, 44, 1, 1, 21, 21, 54] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 270 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479091 none CN(CC1CCN(C(=O)CCC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 42, 44, 47, 54, 54, 54, 54, 72, 72, 172, 183, 201, 201, 201, 201, 54, 33, 42, 13, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 47, 47, 54, 54, 54, 54, 54, 172, 172, 183, 183, 201, 201, 54, 54, 33, 33, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 799 number of broken/clashed sets: 111 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479091 none CN(CC1CCN(C(=O)CCC2=NOC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 12, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 78, 44, 44, 44, 44, 27, 9, 27, 5, 1, 1, 1, 1, 1, 1, 44, 108, 142, 142, 153, 153, 201, 201, 201, 201, 201, 108, 108, 108, 78, 78, 44, 44, 44, 44, 44, 9, 9, 5, 5, 1, 1, 44, 44, 153, 153, 201] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 643 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479091 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479091 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479091/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479091 Building REAL300025479092 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479092' /scratch/stefan/7787258/working/building/REAL300025479092 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479092 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479092/0 /scratch/stefan/7787258/working/building/REAL300025479092 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/995 `/scratch/stefan/7787258/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479092 none CC1=CN=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 15, 15, 15, 15, 29, 34, 34, 41, 41, 73, 112, 201, 201, 201, 201, 201, 15, 2, 2, 2, 1, 1, 5, 5, 15, 15, 15, 15, 15, 29, 29, 34, 34, 34, 73, 73, 201, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 544 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479092 none CC1=CN=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 190, 137, 131, 137, 131, 131, 131, 112, 89, 65, 89, 29, 65, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 190, 190, 131, 131, 131, 131, 131, 112, 112, 89, 89, 89, 29, 29, 1, 131, 131] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 796 number of broken/clashed sets: 102 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479092 none CC1=CN=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 11, 2, 1, 2, 1, 1, 1, 1, 1, 6, 10, 10, 17, 17, 37, 57, 131, 131, 131, 131, 131, 1, 15, 15, 15, 15, 15, 11, 11, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 37, 37, 131, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 47, 48, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 337 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479092 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479092/1 /scratch/stefan/7787258/working/building/REAL300025479092 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/996 `/scratch/stefan/7787258/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C[NH+]=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479092.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479092 none CC1=C[NH+]=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 16, 16, 16, 16, 17, 18, 18, 18, 18, 30, 47, 89, 89, 89, 89, 89, 16, 2, 2, 2, 1, 1, 5, 5, 16, 16, 16, 16, 16, 17, 17, 18, 18, 18, 30, 30, 89, 16, 16] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479092 none CC1=C[NH+]=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 86, 51, 50, 51, 50, 50, 50, 34, 33, 33, 33, 26, 33, 13, 1, 1, 1, 1, 1, 1, 1, 50, 89, 89, 89, 89, 89, 86, 86, 50, 50, 50, 50, 50, 34, 34, 33, 33, 33, 26, 26, 1, 50, 50] 89 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 369 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: REAL300025479092 none CC1=C[NH+]=CN1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 16, 16, 10, 3, 1, 3, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 10, 14, 50, 50, 50, 50, 50, 1, 16, 16, 16, 16, 16, 10, 10, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 10, 10, 50, 1, 1] 89 rigid atoms, others: [35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 48, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479092 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479092 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479092/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479092/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479092 Building REAL300025479093 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479093' /scratch/stefan/7787258/working/building/REAL300025479093 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479093 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479093/0 /scratch/stefan/7787258/working/building/REAL300025479093 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/997 `/scratch/stefan/7787258/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C) `REAL300025479093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 6, 6, 6, 6, 12, 15, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 12, 12, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 50, 51, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 18, 19, 14, 18, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 14, 14, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 12, 15, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 12, 12, 20, 1, 1, 2, 2, 2, 2, 2, 2, 2] 20 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479093 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479093/1 /scratch/stefan/7787258/working/building/REAL300025479093 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/998 `/scratch/stefan/7787258/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C) `REAL300025479093.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 5, 5, 5, 6, 6, 8, 8, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 8, 8, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 49, 50, 51, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54]) total number of confs: 46 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: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 8, 9, 8, 8, 8, 8, 8, 7, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 1, 8, 8, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 20 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: REAL300025479093 none C[C@@H]1[C@H](C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 7, 7, 8, 8, 8, 8, 8, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 8, 1, 1, 3, 3, 3, 3, 3, 3, 3] 9 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 46, 47, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 37 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479093 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479093 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479093/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479093/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479093 Building REAL300025479094 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479094' /scratch/stefan/7787258/working/building/REAL300025479094 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479094 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479094/0 /scratch/stefan/7787258/working/building/REAL300025479094 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/999 `/scratch/stefan/7787258/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479094 none CN(CC1CCN(C(=O)[C@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 13, 33, 33, 61, 88, 155, 155, 155, 155, 155, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 61, 61, 155] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 423 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479094 none CN(CC1CCN(C(=O)[C@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 73, 89, 134, 155, 155, 155, 155, 174, 174, 201, 201, 201, 201, 201, 155, 36, 73, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 134, 134, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 155, 155, 36, 36, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 796 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479094 none CN(CC1CCN(C(=O)[C@H]2CCCO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 33, 70, 70, 113, 145, 201, 201, 201, 201, 201, 33, 33, 33, 20, 20, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 113, 113, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 611 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479094 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479094 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479094/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479094 Building REAL300025479095 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479095' /scratch/stefan/7787258/working/building/REAL300025479095 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479095 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479095/0 /scratch/stefan/7787258/working/building/REAL300025479095 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1000 `/scratch/stefan/7787258/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479095 none CN(CC1CCN(C(=O)CCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 15, 22, 42, 42, 1, 10, 15, 15, 22, 23, 50, 50, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 16, 15, 25, 25, 38, 1, 1, 22, 22, 50] 139 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479095 none CN(CC1CCN(C(=O)CCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 41, 43, 45, 50, 50, 50, 50, 64, 64, 131, 136, 139, 139, 50, 32, 41, 13, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 45, 45, 50, 50, 50, 50, 50, 131, 131, 139, 139, 139, 50, 50, 32, 32, 1] 139 rigid atoms, others: [44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 603 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479095 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479095 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479095/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479095 Building REAL300025479096 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479096' /scratch/stefan/7787258/working/building/REAL300025479096 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479096 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479096/0 /scratch/stefan/7787258/working/building/REAL300025479096 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1001 `/scratch/stefan/7787258/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1) `REAL300025479096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479096 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 3, 3, 5, 5, 5, 5, 10, 14, 14, 21, 21, 48, 82, 186, 186, 186, 186, 186, 5, 1, 1, 1, 10, 10, 10, 6, 6, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 48, 48, 186, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 443 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479096 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 186, 175, 186, 175, 175, 175, 150, 113, 75, 113, 29, 74, 13, 1, 1, 1, 1, 1, 1, 1, 175, 186, 186, 186, 201, 201, 201, 201, 201, 175, 175, 175, 175, 175, 150, 150, 113, 113, 113, 29, 29, 1, 175, 175, 186, 186, 186, 186, 186, 186] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 794 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479096 none COCC1(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 11, 11, 19, 19, 43, 75, 175, 175, 175, 175, 175, 1, 5, 5, 5, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 43, 43, 175, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 45, 46, 23, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 422 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479096 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479096 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479096/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479096 Building REAL300025479097 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479097' /scratch/stefan/7787258/working/building/REAL300025479097 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479097 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479097/0 /scratch/stefan/7787258/working/building/REAL300025479097 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1002 `/scratch/stefan/7787258/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(F)F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479097 none CC(CC(F)F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 6, 7, 7, 1, 3, 1, 1, 1, 1, 1, 6, 10, 10, 18, 18, 43, 74, 167, 167, 167, 167, 167, 1, 5, 5, 5, 5, 6, 6, 7, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 43, 43, 167, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 414 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479097 none CC(CC(F)F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 201, 201, 201, 201, 167, 198, 167, 167, 167, 143, 93, 57, 93, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 143, 143, 93, 93, 93, 27, 27, 1, 167, 167] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 762 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479097 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479097 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479097/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479097 Building REAL300025479098 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479098' /scratch/stefan/7787258/working/building/REAL300025479098 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479098 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479098/0 /scratch/stefan/7787258/working/building/REAL300025479098 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1003 `/scratch/stefan/7787258/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC(F)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479098 none CN(CC1CCN(C(=O)C2=CC(F)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 1, 15, 28, 28, 54, 74, 142, 142, 142, 142, 142, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 1, 1, 54, 54, 142] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479098 none CN(CC1CCN(C(=O)C2=CC(F)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 81, 83, 124, 142, 142, 142, 142, 160, 160, 201, 201, 201, 201, 201, 142, 39, 81, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 124, 124, 142, 142, 142, 142, 142, 201, 201, 201, 142, 142, 39, 39, 1] 201 rigid atoms, others: [43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 709 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479098 none CN(CC1CCN(C(=O)C2=CC(F)=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 29, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 46, 70, 70, 114, 138, 201, 201, 201, 201, 201, 46, 46, 46, 29, 29, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 114, 114, 201] 201 rigid atoms, others: [36, 37, 38, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 603 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479098 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479098 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479098/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479098 Building REAL300025479099 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479099' /scratch/stefan/7787258/working/building/REAL300025479099 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479099 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479099/0 /scratch/stefan/7787258/working/building/REAL300025479099 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1004 `/scratch/stefan/7787258/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479099 none CN(CC1CCN(C(=O)CC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 22, 22, 22, 1, 8, 12, 12, 17, 18, 40, 40, 40, 40, 40, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 22, 22, 22, 22, 22, 22, 22, 1, 1, 17, 17, 40] 93 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479099 none CN(CC1CCN(C(=O)CC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 35, 40, 40, 40, 40, 41, 41, 77, 93, 93, 93, 40, 30, 33, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 35, 35, 40, 40, 40, 40, 40, 77, 77, 93, 93, 93, 93, 93, 93, 93, 40, 40, 30, 30, 1] 93 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 390 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479099 none CN(CC1CCN(C(=O)CC2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [48, 35, 22, 22, 22, 22, 13, 6, 13, 1, 1, 1, 1, 1, 22, 48, 63, 63, 73, 73, 93, 93, 93, 93, 93, 48, 48, 48, 35, 35, 22, 22, 22, 22, 22, 6, 6, 2, 2, 2, 1, 1, 1, 1, 22, 22, 73, 73, 93] 93 rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 326 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479099 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479099 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479099/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479099 Building REAL300025479100 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479100' /scratch/stefan/7787258/working/building/REAL300025479100 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479100 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479100/0 /scratch/stefan/7787258/working/building/REAL300025479100 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1005 `/scratch/stefan/7787258/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479100 none CN(CC1CCN(C(=O)C2(C)CNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 13, 33, 33, 77, 109, 182, 182, 182, 182, 182, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 77, 77, 182] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 491 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479100 none CN(CC1CCN(C(=O)C2(C)CNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 97, 118, 167, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 182, 40, 97, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 167, 167, 182, 182, 182, 182, 182, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 40, 40, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 785 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479100 none CN(CC1CCN(C(=O)C2(C)CNC(=O)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 33, 55, 55, 102, 137, 201, 201, 201, 201, 201, 33, 33, 33, 18, 18, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 102, 102, 201] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49]) total number of confs: 585 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479100 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479100 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479100/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479100 Building REAL300025479101 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479101' /scratch/stefan/7787258/working/building/REAL300025479101 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479101 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479101/0 /scratch/stefan/7787258/working/building/REAL300025479101 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1006 `/scratch/stefan/7787258/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479101 none CN(CC1CCN(C(=O)C2(C)CC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 1, 15, 36, 36, 78, 106, 162, 162, 162, 162, 162, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 78, 78, 162] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 468 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479101 none CN(CC1CCN(C(=O)C2(C)CC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 67, 94, 143, 162, 162, 162, 162, 183, 183, 201, 201, 201, 201, 201, 201, 162, 33, 67, 13, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 143, 143, 162, 162, 162, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 33, 33, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 825 number of broken/clashed sets: 151 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479101 none CN(CC1CCN(C(=O)C2(C)CC3CC3C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 28, 60, 60, 109, 147, 201, 201, 201, 201, 201, 28, 28, 28, 12, 12, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 109, 109, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52]) total number of confs: 611 number of broken/clashed sets: 151 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479101 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479101 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479101/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479101 Building REAL300025479102 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479102' /scratch/stefan/7787258/working/building/REAL300025479102 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479102 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479102/0 /scratch/stefan/7787258/working/building/REAL300025479102 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1007 `/scratch/stefan/7787258/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(CCF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479102 none CN(CC1CCN(C(=O)C2(CCF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 7, 4, 4, 1, 5, 6, 6, 7, 7, 11, 11, 11, 11, 11, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 7, 7, 4, 4, 4, 4, 1, 1, 7, 7, 11] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 60 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: REAL300025479102 none CN(CC1CCN(C(=O)C2(CCF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 13, 13, 13, 13, 13, 11, 10, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 10, 10, 1] 13 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 30 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: REAL300025479102 none CN(CC1CCN(C(=O)C2(CCF)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 4, 6, 1, 1, 4, 8, 9, 9, 10, 10, 13, 13, 13, 13, 13, 8, 8, 8, 6, 6, 4, 4, 4, 4, 4, 4, 4, 6, 6, 1, 1, 1, 1, 4, 4, 10, 10, 13] 13 rigid atoms, others: [7, 40, 9, 10, 43, 13, 14, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479102 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479102 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479102/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479102 Building REAL300025479103 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479103' /scratch/stefan/7787258/working/building/REAL300025479103 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479103 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479103/0 /scratch/stefan/7787258/working/building/REAL300025479103 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1008 `/scratch/stefan/7787258/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479103 none COCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 13, 5, 13, 13, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 17, 17, 23, 29, 52, 52, 52, 52, 52, 1, 21, 21, 21, 19, 19, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 23, 23, 52, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479103 none COCC(C)(C)CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 109, 182, 182, 66, 52, 66, 52, 52, 52, 47, 34, 22, 34, 13, 22, 11, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 182, 109, 109, 52, 52, 52, 52, 52, 47, 47, 34, 34, 34, 13, 13, 1, 52, 52] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 986 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479103 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479103 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479103/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479103 Building REAL300025479104 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479104' /scratch/stefan/7787258/working/building/REAL300025479104 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479104 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479104/0 /scratch/stefan/7787258/working/building/REAL300025479104 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1009 `/scratch/stefan/7787258/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)COCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479104 none CN(CC1CCN(C(=O)COCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 2, 2, 8, 23, 45, 64, 64, 1, 11, 15, 15, 22, 22, 51, 51, 51, 51, 51, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 45, 45, 64, 1, 1, 22, 22, 51] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 388 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479104 none CN(CC1CCN(C(=O)COCC(F)F)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 42, 45, 51, 51, 51, 51, 76, 76, 132, 190, 201, 201, 201, 51, 32, 40, 12, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 45, 45, 51, 51, 51, 51, 51, 132, 132, 201, 201, 201, 51, 51, 32, 32, 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: 723 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479104 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479104 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479104/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479104 Building REAL300025479105 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479105' /scratch/stefan/7787258/working/building/REAL300025479105 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479105 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479105/0 /scratch/stefan/7787258/working/building/REAL300025479105 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1010 `/scratch/stefan/7787258/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@]23C[C@H]2COC3)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479105 none CN(CC1CCN(C(=O)[C@]23C[C@H]2COC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 1, 13, 30, 30, 67, 90, 150, 150, 150, 150, 150, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 67, 67, 150] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 43, 44, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 417 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479105 none CN(CC1CCN(C(=O)[C@]23C[C@H]2COC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 67, 90, 133, 150, 150, 150, 150, 157, 157, 201, 201, 201, 201, 201, 201, 150, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 133, 133, 150, 150, 150, 150, 150, 201, 201, 201, 201, 201, 201, 150, 150, 38, 38, 1] 201 rigid atoms, others: [47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 720 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479105 none CN(CC1CCN(C(=O)[C@]23C[C@H]2COC3)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 27, 55, 55, 106, 140, 201, 201, 201, 201, 201, 27, 27, 27, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 106, 106, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47]) total number of confs: 589 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479105 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479105 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479105/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479105 Building REAL300025479106 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479106' /scratch/stefan/7787258/working/building/REAL300025479106 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300025479106 as failed and skipping /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `/scratch/stefan/7787258/failed' `/scratch/stefan/7787258/working/building/REAL300025479106' -> `/scratch/stefan/7787258/failed/REAL300025479106' Building REAL300025479107 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479107' /scratch/stefan/7787258/working/building/REAL300025479107 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479107 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479107/0 /scratch/stefan/7787258/working/building/REAL300025479107 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1011 `/scratch/stefan/7787258/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479107 none CN(CC1CCN(C(=O)C2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 14, 37, 37, 87, 113, 176, 176, 176, 176, 176, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 87, 87, 176] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 502 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479107 none CN(CC1CCN(C(=O)C2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 72, 109, 157, 176, 176, 176, 176, 200, 200, 201, 201, 201, 176, 39, 72, 13, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 157, 157, 176, 176, 176, 176, 176, 201, 201, 201, 201, 201, 201, 201, 176, 176, 39, 39, 1] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 809 number of broken/clashed sets: 102 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479107 none CN(CC1CCN(C(=O)C2(C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 4, 25, 52, 52, 102, 136, 201, 201, 201, 201, 201, 25, 25, 25, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 4, 4, 102, 102, 201] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 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]) total number of confs: 579 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479107 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479107 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479107/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479107 Building REAL300025479108 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479108' /scratch/stefan/7787258/working/building/REAL300025479108 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479108 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479108/0 /scratch/stefan/7787258/working/building/REAL300025479108 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1012 `/scratch/stefan/7787258/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479108 none CN(CC1CCN(C(=O)C2=CNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 1, 10, 25, 25, 46, 70, 126, 126, 126, 126, 126, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 46, 46, 126] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 39, 34, 14, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 332 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479108 none CN(CC1CCN(C(=O)C2=CNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 73, 78, 114, 126, 126, 126, 126, 135, 135, 201, 201, 201, 201, 126, 36, 73, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 114, 114, 126, 126, 126, 126, 126, 201, 201, 201, 201, 126, 126, 36, 36, 1] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 678 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479108 none CN(CC1CCN(C(=O)C2=CNC=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 11, 34, 62, 62, 97, 130, 201, 201, 201, 201, 201, 34, 34, 34, 21, 21, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 97, 97, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 586 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479108 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479108 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479108/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479108 Building REAL300025479109 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479109' /scratch/stefan/7787258/working/building/REAL300025479109 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479109 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479109/0 /scratch/stefan/7787258/working/building/REAL300025479109 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1013 `/scratch/stefan/7787258/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479109 none CC1CCCC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 21, 21, 21, 21, 38, 48, 48, 49, 49, 86, 121, 201, 201, 201, 201, 201, 21, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 38, 38, 48, 48, 48, 86, 86, 201, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 36, 33, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 589 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479109 none CC1CCCC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 199, 115, 107, 115, 107, 107, 107, 91, 62, 45, 62, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 107, 107, 107, 107, 107, 91, 91, 62, 62, 62, 27, 27, 1, 107, 107] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 858 number of broken/clashed sets: 121 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479109 none CC1CCCC1CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 21, 13, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 22, 36, 107, 107, 107, 107, 107, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 22, 22, 107, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 289 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479109 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479109 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479109/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479109 Building REAL300025479110 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479110' /scratch/stefan/7787258/working/building/REAL300025479110 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479110 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479110/0 /scratch/stefan/7787258/working/building/REAL300025479110 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1014 `/scratch/stefan/7787258/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479110 none CCC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 4, 4, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 4, 7, 7, 10, 10, 24, 38, 107, 107, 107, 107, 107, 1, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 24, 24, 107, 1, 1] 201 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 50, 51, 41, 39, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 270 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479110 none CCC(=O)NC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 132, 132, 132, 132, 130, 132, 107, 130, 107, 107, 107, 98, 64, 47, 64, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 107, 107, 107, 107, 107, 98, 98, 64, 64, 64, 28, 28, 1, 107, 107] 201 rigid atoms, others: [49, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 941 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479110 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479110 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479110/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479110 Building REAL300025479111 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479111' /scratch/stefan/7787258/working/building/REAL300025479111 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479111 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479111/0 /scratch/stefan/7787258/working/building/REAL300025479111 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1015 `/scratch/stefan/7787258/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC(=O)N(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479111 none CN(CC1CCN(C(=O)C2CC(=O)N(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 1, 14, 32, 32, 58, 78, 143, 143, 143, 143, 143, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 58, 58, 143] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 384 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: REAL300025479111 none CN(CC1CCN(C(=O)C2CC(=O)N(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 74, 86, 126, 143, 143, 143, 143, 152, 152, 201, 201, 201, 201, 201, 201, 143, 39, 74, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 126, 126, 143, 143, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 39, 39, 1] 201 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 805 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: REAL300025479111 none CN(CC1CCN(C(=O)C2CC(=O)N(C)C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 42, 71, 71, 107, 134, 201, 201, 201, 201, 201, 42, 42, 42, 23, 23, 10, 10, 10, 10, 10, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 107, 107, 201] 201 rigid atoms, others: [43, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39, 44] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 581 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479111 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479111 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479111/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479111 Building REAL300025479112 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479112' /scratch/stefan/7787258/working/building/REAL300025479112 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479112 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479112/0 /scratch/stefan/7787258/working/building/REAL300025479112 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1016 `/scratch/stefan/7787258/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1) `REAL300025479112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479112 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 8, 8, 9, 9, 23, 37, 97, 97, 97, 97, 97, 1, 18, 18, 18, 18, 18, 18, 18, 14, 14, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 23, 23, 97, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 45, 46, 35, 22] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 281 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479112 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 5, 11, 11, 18, 18, 18, 18, 34, 46, 46, 48, 48, 86, 121, 201, 201, 201, 201, 201, 18, 1, 1, 1, 2, 2, 2, 2, 5, 5, 18, 18, 18, 18, 18, 34, 34, 46, 46, 46, 86, 86, 201, 18, 18, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 47, 48, 49, 50, 51, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 587 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: REAL300025479112 none CC(CC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 107, 97, 107, 97, 97, 97, 88, 60, 45, 60, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97, 97, 88, 88, 60, 60, 60, 28, 28, 1, 97, 97, 201, 201, 201, 201, 201] 201 rigid atoms, others: [44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 812 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479112 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479112 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479112/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479112 Building REAL300025479113 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479113' /scratch/stefan/7787258/working/building/REAL300025479113 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479113 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479113/0 /scratch/stefan/7787258/working/building/REAL300025479113 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1017 `/scratch/stefan/7787258/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C3CC3)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.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: REAL300025479113 none CN(CC1CCN(C(=O)C2(C3CC3)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 12, 32, 32, 60, 91, 170, 170, 170, 170, 170, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 60, 60, 170] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 425 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479113 none CN(CC1CCN(C(=O)C2(C3CC3)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 89, 101, 150, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 170, 41, 89, 13, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 150, 150, 170, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 41, 41, 1] 201 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 784 number of broken/clashed sets: 65 ./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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479113 none CN(CC1CCN(C(=O)C2(C3CC3)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 19, 46, 46, 85, 121, 201, 201, 201, 201, 201, 19, 19, 19, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 85, 85, 201] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 533 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479113 none CN(CC1CCN(C(=O)C2(C3CC3)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 3, 3, 3, 3, 2, 1, 2, 1, 1, 2, 2, 1, 1, 1, 3, 19, 46, 46, 85, 121, 201, 201, 201, 201, 201, 19, 19, 19, 9, 9, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 85, 85, 201] 201 rigid atoms, others: [45, 7, 9, 10, 43, 44, 13, 14, 15, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52]) total number of confs: 537 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479113 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479113 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479113/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479113 Building REAL300025479114 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479114' /scratch/stefan/7787258/working/building/REAL300025479114 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479114 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479114/0 /scratch/stefan/7787258/working/building/REAL300025479114 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1018 `/scratch/stefan/7787258/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1) `REAL300025479114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479114 none COC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 6, 6, 5, 6, 16, 24, 24, 30, 30, 60, 88, 201, 201, 201, 201, 201, 5, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 16, 16, 24, 24, 24, 60, 60, 201, 5, 5, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 45, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479114 none COC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 195, 159, 195, 159, 159, 159, 144, 99, 68, 99, 28, 68, 12, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 144, 144, 99, 99, 99, 28, 28, 1, 159, 159, 201] 201 rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 763 number of broken/clashed sets: 85 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479114 none COC1=NC(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 15, 15, 36, 56, 159, 159, 159, 159, 159, 1, 5, 5, 8, 7, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 36, 36, 159, 1, 1, 5] 201 rigid atoms, others: [32, 33, 34, 43, 5, 7, 8, 9, 10, 11, 44, 24, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 351 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479114 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479114 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479114/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479114 Building REAL300025479115 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479115' /scratch/stefan/7787258/working/building/REAL300025479115 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479115 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479115/0 /scratch/stefan/7787258/working/building/REAL300025479115 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1019 `/scratch/stefan/7787258/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C(C)(C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479115 none CN(CC1CCN(C(=O)C(C)(C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 1, 13, 27, 27, 50, 76, 135, 135, 135, 135, 135, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 50, 50, 135] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 50, 35, 36, 51] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 365 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479115 none CN(CC1CCN(C(=O)C(C)(C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 70, 78, 120, 135, 135, 135, 135, 199, 199, 201, 201, 201, 201, 201, 201, 135, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 120, 120, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 135, 37, 37, 1] 201 rigid atoms, others: [54, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 774 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479115 none CN(CC1CCN(C(=O)C(C)(C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 7, 7, 7, 7, 4, 4, 4, 1, 4, 4, 1, 1, 1, 1, 7, 31, 54, 54, 100, 139, 201, 201, 201, 201, 201, 31, 31, 31, 17, 17, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 100, 100, 201] 201 rigid atoms, others: [45, 9, 43, 12, 13, 14, 15, 48, 49, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 50, 51, 52, 53, 54]) total number of confs: 592 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479115 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479115 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479115/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479115 Building REAL300025479116 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479116' /scratch/stefan/7787258/working/building/REAL300025479116 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479116 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479116/0 /scratch/stefan/7787258/working/building/REAL300025479116 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1020 `/scratch/stefan/7787258/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1) `REAL300025479116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479116 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 12, 12, 31, 49, 125, 125, 125, 125, 125, 1, 10, 12, 12, 12, 12, 12, 12, 10, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 31, 31, 125, 1, 1, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 44, 45, 35, 22, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 320 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479116 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 1, 4, 8, 8, 12, 12, 12, 12, 25, 31, 31, 38, 38, 72, 112, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 8, 8, 8, 4, 12, 12, 12, 12, 12, 25, 25, 31, 31, 31, 72, 72, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 46, 47, 48, 49, 50, 51, 52, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 545 number of broken/clashed sets: 97 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479116 none COC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 125, 161, 125, 125, 125, 106, 76, 55, 76, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 106, 106, 76, 76, 76, 28, 28, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 841 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479116 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479116 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479116/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479116 Building REAL300025479117 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479117' /scratch/stefan/7787258/working/building/REAL300025479117 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479117 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479117/0 /scratch/stefan/7787258/working/building/REAL300025479117 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1021 `/scratch/stefan/7787258/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CSN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479117 none CN(CC1CCN(C(=O)C2=CSN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 2, 2, 5, 4, 5, 5, 1, 14, 31, 31, 55, 83, 158, 158, 158, 158, 158, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 5, 1, 1, 55, 55, 158] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 36, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 38, 39, 40]) total number of confs: 394 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479117 none CN(CC1CCN(C(=O)C2=CSN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 67, 76, 133, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 158, 37, 67, 13, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 133, 133, 158, 158, 158, 158, 158, 201, 158, 158, 37, 37, 1] 201 rigid atoms, others: [40, 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]) total number of confs: 818 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479117 none CN(CC1CCN(C(=O)C2=CSN=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 5, 31, 57, 57, 97, 138, 201, 201, 201, 201, 201, 31, 31, 31, 16, 16, 5, 5, 5, 5, 5, 1, 5, 5, 97, 97, 201] 201 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 564 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479117 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479117 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479117/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479117 Building REAL300025479118 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479118' /scratch/stefan/7787258/working/building/REAL300025479118 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479118 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479118/0 /scratch/stefan/7787258/working/building/REAL300025479118 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1022 `/scratch/stefan/7787258/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479118 none CN(CC1CCN(C(=O)C2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 14, 39, 39, 84, 113, 177, 177, 177, 177, 177, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 84, 84, 177] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 48, 35, 47, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 493 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479118 none CN(CC1CCN(C(=O)C2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 113, 155, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 177, 39, 80, 13, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 155, 155, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 39, 39, 1] 201 rigid atoms, others: [51, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 800 number of broken/clashed sets: 101 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479118 none CN(CC1CCN(C(=O)C2(C)CCCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 22, 50, 50, 99, 134, 201, 201, 201, 201, 201, 22, 22, 22, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 99, 99, 201] 201 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 46, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 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, 47, 48, 49, 50, 51]) total number of confs: 572 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479118 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479118 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479118/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479118 Building REAL300025479119 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479119' /scratch/stefan/7787258/working/building/REAL300025479119 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479119 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479119/0 /scratch/stefan/7787258/working/building/REAL300025479119 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1023 `/scratch/stefan/7787258/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CN=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479119 none CN(CC1CCN(C(=O)C2=CN=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 1, 12, 29, 29, 59, 88, 162, 162, 162, 162, 162, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 1, 59, 59, 162] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 14, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 39, 40, 41]) total number of confs: 423 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479119 none CN(CC1CCN(C(=O)C2=CN=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 75, 83, 139, 162, 162, 162, 162, 201, 201, 201, 201, 201, 201, 162, 39, 75, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 139, 139, 162, 162, 162, 162, 162, 201, 201, 162, 162, 39, 39, 1] 201 rigid atoms, others: [41, 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]) total number of confs: 815 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479119 none CN(CC1CCN(C(=O)C2=CN=CO2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 5, 23, 50, 50, 92, 129, 201, 201, 201, 201, 201, 23, 23, 23, 12, 12, 5, 5, 5, 5, 5, 1, 1, 5, 5, 92, 92, 201] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 565 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479119 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479119 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479119/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479119 Building REAL300025479120 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479120' /scratch/stefan/7787258/working/building/REAL300025479120 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479120 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479120/0 /scratch/stefan/7787258/working/building/REAL300025479120 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1024 `/scratch/stefan/7787258/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCN2C=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479120 none CN(CC1CCN(C(=O)CCN2C=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 4, 4, 19, 23, 49, 49, 49, 49, 1, 9, 14, 14, 23, 24, 48, 48, 48, 48, 48, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 19, 19, 23, 23, 49, 49, 49, 1, 1, 23, 23, 48] 174 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 262 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479120 none CN(CC1CCN(C(=O)CCN2C=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [39, 37, 39, 42, 48, 48, 48, 48, 65, 65, 102, 106, 174, 174, 174, 174, 48, 28, 37, 12, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 42, 42, 48, 48, 48, 48, 48, 102, 102, 106, 106, 174, 174, 174, 48, 48, 28, 28, 1] 174 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 581 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479120 none CN(CC1CCN(C(=O)CCN2C=CN=C2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [94, 75, 49, 49, 49, 49, 30, 13, 30, 8, 1, 1, 1, 1, 1, 1, 49, 94, 112, 112, 131, 131, 174, 174, 174, 174, 174, 94, 94, 94, 75, 75, 49, 49, 49, 49, 49, 13, 13, 8, 8, 1, 1, 1, 49, 49, 131, 131, 174] 174 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 569 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479120 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479120 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479120/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479120 Building REAL300025479121 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479121' /scratch/stefan/7787258/working/building/REAL300025479121 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479121 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479121/0 /scratch/stefan/7787258/working/building/REAL300025479121 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1025 `/scratch/stefan/7787258/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479121 none CNC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 7, 2, 1, 2, 1, 1, 1, 1, 1, 5, 7, 7, 11, 11, 24, 39, 123, 123, 123, 123, 123, 1, 11, 11, 11, 11, 10, 7, 7, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 24, 24, 123, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479121 none CNC(=O)NCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 123, 167, 123, 123, 123, 113, 75, 53, 75, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 113, 113, 75, 75, 75, 29, 29, 1, 123, 123] 201 rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 857 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479121 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479121 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479121/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479121 Building REAL300025479122 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479122' /scratch/stefan/7787258/working/building/REAL300025479122 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479122 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479122/0 /scratch/stefan/7787258/working/building/REAL300025479122 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1026 `/scratch/stefan/7787258/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=CNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 3, 3, 15, 21, 43, 43, 43, 43, 1, 6, 8, 8, 10, 10, 32, 32, 32, 32, 32, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 15, 15, 21, 21, 43, 43, 43, 1, 1, 10, 10, 32] 111 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 28, 32, 32, 32, 32, 43, 43, 95, 100, 111, 111, 111, 111, 32, 25, 27, 13, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 28, 28, 32, 32, 32, 32, 32, 95, 95, 100, 100, 111, 111, 111, 32, 32, 25, 25, 1] 111 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CNC=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [74, 54, 43, 43, 43, 43, 30, 12, 30, 8, 1, 1, 1, 1, 1, 1, 43, 74, 86, 86, 89, 89, 111, 111, 111, 111, 111, 74, 74, 74, 54, 54, 43, 43, 43, 43, 43, 12, 12, 8, 8, 1, 1, 1, 43, 43, 89, 89, 111] 111 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 369 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479122 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479122/1 /scratch/stefan/7787258/working/building/REAL300025479122 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1027 `/scratch/stefan/7787258/working/3D/1027' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479122.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 2, 2, 13, 18, 25, 25, 25, 25, 1, 7, 11, 11, 13, 13, 24, 24, 24, 24, 24, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 13, 13, 18, 18, 25, 25, 25, 1, 1, 13, 13, 24] 84 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 24, 24, 24, 24, 29, 29, 70, 73, 84, 84, 84, 84, 24, 20, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 24, 24, 24, 24, 24, 70, 70, 73, 73, 84, 84, 84, 24, 24, 20, 20, 1] 84 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479122 none CN(CC1CCN(C(=O)CCC2=CN=CN2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [48, 40, 25, 25, 25, 25, 19, 7, 19, 4, 1, 1, 1, 1, 1, 1, 25, 48, 58, 58, 60, 60, 84, 84, 84, 84, 84, 48, 48, 48, 40, 40, 25, 25, 25, 25, 25, 7, 7, 4, 4, 1, 1, 1, 25, 25, 60, 60, 84] 84 rigid atoms, others: [43, 41, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 268 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479122 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479122 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479122/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479122/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479122 Building REAL300025479123 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479123' /scratch/stefan/7787258/working/building/REAL300025479123 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479123 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479123/0 /scratch/stefan/7787258/working/building/REAL300025479123 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1028 `/scratch/stefan/7787258/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C[N@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 5, 6, 6, 6, 7, 7, 7, 1, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 6, 9] 12 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 56 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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 12, 12, 12, 12, 12, 12, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 1] 12 rigid atoms, others: [54, 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, 19, 20, 28, 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: 35 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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 2, 1, 1, 1, 1, 7, 9, 9, 9, 10, 10, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 12] 12 rigid atoms, others: [48, 45, 10, 43, 44, 13, 14, 15, 16, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 50, 51, 52, 53, 54]) total number of confs: 54 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479123 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479123/1 /scratch/stefan/7787258/working/building/REAL300025479123 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1029 `/scratch/stefan/7787258/working/3D/1029' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C[N@@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479123.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 7, 7, 7, 1, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 6, 9] 11 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 52 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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 11, 11, 11, 11, 11, 11, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 1] 11 rigid atoms, others: [54, 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, 19, 20, 28, 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: 29 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: REAL300025479123 none CN(CC1CCN(C(=O)C[N@@H+](C)C2CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 7, 7, 7, 7, 4, 7, 3, 1, 3, 3, 1, 1, 1, 1, 7, 8, 8, 8, 9, 9, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 11] 11 rigid atoms, others: [48, 45, 10, 43, 44, 13, 14, 15, 16, 49, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 50, 51, 52, 53, 54]) total number of confs: 42 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479123 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479123 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479123/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479123/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479123 Building REAL300025479124 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479124' /scratch/stefan/7787258/working/building/REAL300025479124 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479124 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479124/0 /scratch/stefan/7787258/working/building/REAL300025479124 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1030 `/scratch/stefan/7787258/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479124 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 1, 15, 33, 33, 58, 85, 153, 153, 153, 153, 153, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 58, 58, 153] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44]) total number of confs: 398 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479124 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 66, 84, 132, 153, 153, 153, 153, 200, 200, 201, 201, 201, 201, 201, 201, 153, 33, 66, 13, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 132, 132, 153, 153, 153, 153, 153, 201, 201, 201, 153, 153, 33, 33, 1] 201 rigid atoms, others: [44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 805 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479124 none CN(CC1CCN(C(=O)C2=CC=C(F)C=N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 32, 62, 62, 104, 141, 201, 201, 201, 201, 201, 32, 32, 32, 17, 17, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 104, 104, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 585 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479124 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479124 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479124/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479124 Building REAL300025479125 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479125' /scratch/stefan/7787258/working/building/REAL300025479125 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479125 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479125/0 /scratch/stefan/7787258/working/building/REAL300025479125 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1031 `/scratch/stefan/7787258/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479125 none C=CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 62, 33, 27, 18, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 9, 9, 12, 14, 29, 29, 29, 29, 29, 1, 67, 67, 67, 62, 62, 33, 33, 18, 18, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 12, 12, 29, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 345 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479125 none C=CCCOCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 120, 109, 31, 29, 31, 29, 29, 29, 28, 22, 21, 22, 14, 21, 11, 1, 1, 1, 1, 1, 1, 1, 29, 201, 201, 201, 201, 201, 122, 122, 109, 109, 29, 29, 29, 29, 29, 28, 28, 22, 22, 22, 14, 14, 1, 29, 29] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 802 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479125 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479125 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479125/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479125 Building REAL300025479126 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479126' /scratch/stefan/7787258/working/building/REAL300025479126 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479126 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479126/0 /scratch/stefan/7787258/working/building/REAL300025479126 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1032 `/scratch/stefan/7787258/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479126 none C=CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 11, 7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 12, 12, 27, 37, 91, 91, 91, 91, 91, 1, 30, 30, 30, 22, 22, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 27, 27, 91, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 48, 49, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 323 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479126 none C=CCOC(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 141, 136, 93, 136, 91, 93, 91, 91, 91, 75, 57, 36, 57, 18, 36, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 136, 136, 136, 136, 91, 91, 91, 91, 91, 75, 75, 57, 57, 57, 18, 18, 1, 91, 91] 201 rigid atoms, others: [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, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 942 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479126 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479126 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479126/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479126 Building REAL300025479127 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479127' /scratch/stefan/7787258/working/building/REAL300025479127 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479127 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479127/0 /scratch/stefan/7787258/working/building/REAL300025479127 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1033 `/scratch/stefan/7787258/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479127 none CC(C)OCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 65, 90, 47, 18, 14, 2, 1, 2, 1, 1, 1, 1, 1, 4, 7, 7, 8, 8, 9, 12, 33, 33, 33, 33, 33, 1, 90, 90, 90, 90, 90, 90, 90, 43, 43, 22, 22, 14, 14, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 9, 9, 33, 1, 1] 201 rigid atoms, others: [43, 7, 40, 9, 10, 11, 12, 13, 44, 53, 54, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 469 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: REAL300025479127 none CC(C)OCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 197, 123, 117, 40, 33, 40, 33, 33, 33, 28, 28, 27, 28, 13, 27, 9, 1, 1, 1, 1, 1, 1, 1, 33, 201, 201, 201, 201, 201, 201, 201, 186, 187, 141, 141, 117, 117, 33, 33, 33, 33, 33, 28, 28, 28, 28, 28, 13, 13, 1, 33, 33] 201 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 913 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479127 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479127 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479127/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479127 Building REAL300025479128 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479128' /scratch/stefan/7787258/working/building/REAL300025479128 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479128 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479128/0 /scratch/stefan/7787258/working/building/REAL300025479128 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1034 `/scratch/stefan/7787258/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479128 none CN(CC1CCN(C(=O)CCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 1, 3, 3, 14, 21, 43, 72, 72, 1, 7, 9, 9, 11, 11, 28, 28, 28, 28, 28, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 14, 14, 25, 25, 39, 39, 72, 72, 1, 1, 11, 11, 28] 178 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 45, 44, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 356 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479128 none CN(CC1CCN(C(=O)CCCC(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 25, 28, 28, 28, 28, 39, 39, 107, 116, 165, 178, 178, 28, 22, 24, 12, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 25, 25, 28, 28, 28, 28, 28, 107, 107, 136, 136, 156, 155, 178, 178, 28, 28, 22, 22, 1] 178 rigid atoms, others: [48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 859 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479128 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479128 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479128/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479128 Building REAL300025479129 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479129' /scratch/stefan/7787258/working/building/REAL300025479129 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479129 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479129/0 /scratch/stefan/7787258/working/building/REAL300025479129 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1035 `/scratch/stefan/7787258/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479129 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 6, 12, 12, 16, 19, 27, 27, 27, 27, 27, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 16, 16, 27] 28 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 17, 50, 35, 36, 51, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 92 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479129 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 26, 26, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 27, 19, 24, 12, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 19, 19, 1] 28 rigid atoms, others: [54, 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, 19, 20, 28, 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: 82 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479129 none CN(CC1CCN(C(=O)C2CC[NH+](C)CC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 18, 18, 24, 24, 28, 28, 28, 28, 28, 13, 13, 13, 8, 8, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 24, 24, 28] 28 rigid atoms, others: [48, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 49, 46, 41, 39, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479129 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479129 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479129/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479129 Building REAL300025479130 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479130' /scratch/stefan/7787258/working/building/REAL300025479130 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479130 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479130/0 /scratch/stefan/7787258/working/building/REAL300025479130 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1036 `/scratch/stefan/7787258/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479130 none CC1=NNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 26, 37, 37, 50, 50, 76, 116, 201, 201, 201, 201, 201, 10, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 26, 26, 37, 37, 37, 76, 76, 201, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 546 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: REAL300025479130 none CC1=NNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 158, 138, 158, 138, 138, 138, 117, 87, 64, 87, 28, 64, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 117, 117, 87, 87, 87, 28, 28, 1, 138, 138] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 687 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: REAL300025479130 none CC1=NNC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 6, 11, 11, 21, 21, 40, 65, 138, 138, 138, 138, 138, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 40, 40, 138, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 336 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479130 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479130 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479130/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479130 Building REAL300025479131 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479131' /scratch/stefan/7787258/working/building/REAL300025479131 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479131 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479131/0 /scratch/stefan/7787258/working/building/REAL300025479131 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1037 `/scratch/stefan/7787258/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1) `REAL300025479131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479131 none C#CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 20, 27, 27, 36, 36, 72, 109, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 27, 27, 27, 72, 72, 201, 7, 7, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 527 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479131 none C#CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 182, 201, 182, 182, 182, 146, 89, 54, 89, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 182, 201, 201, 201, 201, 201, 182, 182, 182, 182, 182, 146, 146, 89, 89, 89, 28, 28, 1, 182, 182, 201, 201] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 779 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: REAL300025479131 none C#CC1=CC=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 26, 26, 54, 87, 182, 182, 182, 182, 182, 1, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 54, 54, 182, 1, 1, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 451 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479131 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479131 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479131/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479131 Building REAL300025479132 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479132' /scratch/stefan/7787258/working/building/REAL300025479132 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479132 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479132/0 /scratch/stefan/7787258/working/building/REAL300025479132 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1038 `/scratch/stefan/7787258/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479132 none CC1=NNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 24, 39, 39, 55, 55, 81, 122, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 8, 8, 8, 8, 8, 24, 24, 39, 39, 39, 81, 81, 201, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 545 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: REAL300025479132 none CC1=NNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 188, 161, 188, 161, 161, 161, 142, 98, 64, 98, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 201, 161, 161, 161, 161, 161, 142, 142, 98, 98, 98, 30, 30, 1, 161, 161] 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, 43, 44]) total number of confs: 743 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: REAL300025479132 none CC1=NNN=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 1, 1, 6, 14, 14, 28, 28, 51, 78, 161, 161, 161, 161, 161, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 51, 51, 161, 1, 1] 201 rigid atoms, others: [32, 33, 34, 43, 6, 8, 9, 10, 11, 12, 44, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 387 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479132 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479132/1 /scratch/stefan/7787258/working/building/REAL300025479132 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1039 `/scratch/stefan/7787258/working/3D/1039' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1) `REAL300025479132.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479132 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 32, 44, 44, 53, 53, 80, 120, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 32, 32, 44, 44, 44, 80, 80, 201, 11, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 44, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479132 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 123, 152, 123, 123, 123, 109, 74, 57, 74, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 109, 109, 74, 74, 74, 29, 29, 1, 123, 123, 201] 201 rigid atoms, others: [41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 679 number of broken/clashed sets: 65 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479132 none CC1=C(C(=O)N2CCC(CN(C)C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 3, 1, 1, 1, 1, 1, 5, 10, 10, 17, 17, 37, 58, 123, 123, 123, 123, 123, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 37, 37, 123, 1, 1, 11] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 22, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 302 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479132 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479132 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479132/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479132/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479132 Building REAL300025479133 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479133' /scratch/stefan/7787258/working/building/REAL300025479133 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479133 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479133/0 /scratch/stefan/7787258/working/building/REAL300025479133 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1040 `/scratch/stefan/7787258/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479133 none CCCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 3, 10, 15, 1, 3, 1, 1, 1, 1, 1, 5, 8, 8, 11, 11, 27, 40, 103, 103, 103, 103, 103, 1, 28, 28, 28, 28, 28, 26, 26, 10, 15, 15, 15, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 27, 27, 103, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 356 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479133 none CCCC(OC)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 185, 106, 185, 187, 103, 106, 103, 103, 103, 90, 71, 45, 71, 20, 45, 12, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 185, 187, 187, 187, 103, 103, 103, 103, 103, 90, 90, 71, 71, 71, 20, 20, 1, 103, 103] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 896 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479133 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479133 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479133/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479133 Building REAL300025479134 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479134' /scratch/stefan/7787258/working/building/REAL300025479134 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479134 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479134/0 /scratch/stefan/7787258/working/building/REAL300025479134 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1041 `/scratch/stefan/7787258/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479134 none C=C(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 13, 13, 33, 33, 62, 96, 176, 176, 176, 176, 176, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 62, 62, 176, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 12, 40, 50, 51, 41, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 457 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479134 none C=C(C)C(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 176, 201, 176, 176, 176, 162, 114, 65, 114, 28, 65, 12, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 176, 162, 162, 114, 114, 114, 28, 28, 1, 176, 176] 201 rigid atoms, others: [49, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 729 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479134 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479134 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479134/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479134 Building REAL300025479135 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479135' /scratch/stefan/7787258/working/building/REAL300025479135 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479135 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479135/0 /scratch/stefan/7787258/working/building/REAL300025479135 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1042 `/scratch/stefan/7787258/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479135 none CC(CC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 8, 12, 12, 1, 3, 1, 1, 1, 1, 1, 5, 9, 9, 15, 15, 34, 56, 149, 149, 149, 149, 149, 1, 5, 5, 5, 5, 8, 8, 12, 12, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 34, 34, 149, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 373 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479135 none CC(CC(N)=O)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 149, 201, 149, 149, 149, 121, 84, 57, 84, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 121, 121, 84, 84, 84, 30, 30, 1, 149, 149] 201 rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 764 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479135 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479135 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479135/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479135 Building REAL300025479136 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479136' /scratch/stefan/7787258/working/building/REAL300025479136 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479136 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479136/0 /scratch/stefan/7787258/working/building/REAL300025479136 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1043 `/scratch/stefan/7787258/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCC2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479136 none CN(CC1CCN(C(=O)C2CCC2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 12, 12, 1, 7, 11, 11, 13, 13, 23, 23, 23, 23, 23, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 12, 12, 1, 1, 13, 13, 23] 34 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 46, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479136 none CN(CC1CCN(C(=O)C2CCC2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 20, 21, 21, 23, 23, 23, 23, 29, 29, 30, 30, 30, 30, 34, 34, 23, 17, 20, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 34, 34, 23, 23, 17, 17, 1] 34 rigid atoms, others: [49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479136 none CN(CC1CCN(C(=O)C2CCC2C(N)=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 13, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 7, 15, 19, 19, 22, 22, 30, 30, 30, 30, 30, 15, 15, 15, 13, 13, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 22, 22, 30] 34 rigid atoms, others: [37, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479136 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479136 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479136/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479136 Building REAL300025479137 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479137' /scratch/stefan/7787258/working/building/REAL300025479137 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479137 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479137/0 /scratch/stefan/7787258/working/building/REAL300025479137 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1044 `/scratch/stefan/7787258/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479137 none CN(CC1CCN(C(=O)C2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 15, 35, 35, 73, 100, 163, 163, 163, 163, 163, 15, 15, 15, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 73, 73, 163] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 15, 35, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 455 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479137 none CN(CC1CCN(C(=O)C2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 76, 102, 144, 163, 163, 163, 163, 187, 187, 201, 201, 201, 201, 201, 163, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 144, 144, 163, 163, 163, 163, 163, 201, 201, 201, 201, 201, 201, 163, 163, 31, 31, 1] 201 rigid atoms, others: [46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 797 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479137 none CN(CC1CCN(C(=O)C2CCNC2=O)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 35, 66, 66, 113, 147, 201, 201, 201, 201, 201, 35, 35, 35, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 113, 113, 201] 201 rigid atoms, others: [36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 614 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479137 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479137 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479137/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479137 Building REAL300025479138 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479138' /scratch/stefan/7787258/working/building/REAL300025479138 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479138 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479138/0 /scratch/stefan/7787258/working/building/REAL300025479138 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1045 `/scratch/stefan/7787258/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2=CNC(=O)N2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479138 none CN(CC1CCN(C(=O)C2=CNC(=O)N2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 1, 13, 30, 30, 61, 87, 151, 151, 151, 151, 151, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 61, 61, 151] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 42, 43, 34, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 400 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: REAL300025479138 none CN(CC1CCN(C(=O)C2=CNC(=O)N2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 83, 99, 139, 151, 151, 151, 151, 169, 169, 201, 201, 201, 201, 201, 201, 151, 41, 83, 13, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 139, 139, 151, 151, 151, 151, 151, 201, 201, 201, 201, 201, 151, 151, 41, 41, 1] 201 rigid atoms, others: [46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 727 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: REAL300025479138 none CN(CC1CCN(C(=O)C2=CNC(=O)N2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 26, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 46, 78, 78, 116, 147, 201, 201, 201, 201, 201, 46, 46, 46, 26, 26, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 11, 11, 116, 116, 201] 201 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 604 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479138 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479138 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479138/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479138 Building REAL300025479139 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479139' /scratch/stefan/7787258/working/building/REAL300025479139 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479139 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479139/0 /scratch/stefan/7787258/working/building/REAL300025479139 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1046 `/scratch/stefan/7787258/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479139 none CN(CC1CCN(C(=O)C2CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 1, 16, 30, 30, 60, 87, 148, 148, 148, 148, 148, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 60, 60, 148] 184 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 45, 16, 35, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 403 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479139 none CN(CC1CCN(C(=O)C2CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [91, 79, 91, 129, 148, 148, 148, 148, 150, 150, 184, 184, 184, 184, 184, 184, 148, 39, 79, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 129, 129, 148, 148, 148, 148, 148, 184, 184, 184, 184, 184, 184, 184, 148, 148, 39, 39, 1] 184 rigid atoms, others: [48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 715 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479139 none CN(CC1CCN(C(=O)C2CN(C)C(=O)N2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 13, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 13, 39, 60, 60, 95, 126, 184, 184, 184, 184, 184, 39, 39, 39, 23, 23, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 1, 13, 13, 95, 95, 184] 184 rigid atoms, others: [43, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 537 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479139 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479139 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479139/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479139 Building REAL300025479140 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479140' /scratch/stefan/7787258/working/building/REAL300025479140 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479140 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479140/0 /scratch/stefan/7787258/working/building/REAL300025479140 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1047 `/scratch/stefan/7787258/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479140 none C=CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 12, 12, 28, 28, 56, 92, 184, 184, 184, 184, 184, 1, 7, 7, 7, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 56, 56, 184, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 47, 48, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 442 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479140 none C=CC(C)(C)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 184, 201, 184, 184, 184, 165, 117, 71, 117, 28, 71, 12, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 184, 184, 184, 165, 165, 117, 117, 117, 28, 28, 1, 184, 184] 201 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 764 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479140 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479140 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479140/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479140 Building REAL300025479141 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479141' /scratch/stefan/7787258/working/building/REAL300025479141 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479141 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479141/0 /scratch/stefan/7787258/working/building/REAL300025479141 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1048 `/scratch/stefan/7787258/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479141 none C#CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 19, 14, 2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 14, 18, 68, 68, 68, 68, 68, 1, 28, 29, 29, 20, 20, 21, 21, 20, 20, 14, 14, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 14, 14, 68, 1, 1] 201 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 51, 52, 41, 39, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 262 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479141 none C#CCCCCCC(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 170, 170, 170, 155, 77, 68, 77, 68, 68, 68, 62, 53, 42, 53, 31, 42, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 170, 170, 170, 170, 170, 170, 155, 155, 68, 68, 68, 68, 68, 62, 62, 53, 53, 53, 31, 31, 1, 68, 68] 201 rigid atoms, others: [50, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52]) total number of confs: 890 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479141 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479141 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479141/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479141 Building REAL300025479142 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479142' /scratch/stefan/7787258/working/building/REAL300025479142 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025479142 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479142/0 /scratch/stefan/7787258/working/building/REAL300025479142 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1049 `/scratch/stefan/7787258/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 6, 7, 7, 9, 9, 13, 13, 13, 13, 13, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 9, 13] 13 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 48, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 53 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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 11, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 1] 13 rigid atoms, others: [51, 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, 19, 20, 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: 26 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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 10, 10, 13, 13, 13, 13, 13, 7, 7, 7, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 13] 13 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479142 /scratch/stefan/7787258/working /scratch/stefan/7787258 mkdir: created directory `1' /scratch/stefan/7787258/working/building/REAL300025479142/1 /scratch/stefan/7787258/working/building/REAL300025479142 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 1 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1050 `/scratch/stefan/7787258/working/3D/1050' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@H]2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479142.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025479142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 10, 10, 15, 16, 18, 18, 18, 18, 18, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 15, 15, 18] 18 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 47, 48, 17, 35, 36, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 18, 12, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 1] 18 rigid atoms, others: [51, 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, 19, 20, 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: 43 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: REAL300025479142 none CN(CC1CCN(C(=O)[C@H]2CCC[N@H+]2C)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 10, 10, 15, 16, 18, 18, 18, 18, 18, 5, 5, 5, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 18] 18 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479142 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479142 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 1: /scratch/stefan/7787258/working/building/REAL300025479142/1.* 0: /scratch/stefan/7787258/working/building/REAL300025479142/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479142 Building REAL300025479143 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479143' /scratch/stefan/7787258/working/building/REAL300025479143 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479143 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479143/0 /scratch/stefan/7787258/working/building/REAL300025479143 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1051 `/scratch/stefan/7787258/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479143 none C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 24, 35, 35, 42, 42, 74, 116, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 24, 24, 35, 35, 35, 74, 74, 201, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 541 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479143 none C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 137, 201, 128, 137, 128, 128, 128, 114, 81, 54, 81, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 201, 201, 128, 128, 128, 128, 128, 114, 114, 81, 81, 81, 29, 29, 1, 128, 128] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 781 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479143 none C[C@@H]1C[C@H]1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 2, 11, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 32, 53, 128, 128, 128, 128, 128, 1, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 128, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 310 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479143 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479143 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479143/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479143 Building REAL300025479144 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479144' /scratch/stefan/7787258/working/building/REAL300025479144 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479144 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479144/0 /scratch/stefan/7787258/working/building/REAL300025479144 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1052 `/scratch/stefan/7787258/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CC2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479144 none CN(CC1CCN(C(=O)CC2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 32, 32, 32, 32, 32, 1, 8, 10, 10, 14, 14, 35, 35, 35, 35, 35, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 14, 14, 35] 116 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 16, 49, 35, 48, 36] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479144 none CN(CC1CCN(C(=O)CC2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 31, 35, 35, 35, 35, 42, 42, 103, 116, 116, 116, 116, 116, 35, 26, 28, 13, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 31, 31, 35, 35, 35, 35, 35, 103, 103, 116, 116, 116, 116, 116, 116, 116, 116, 116, 35, 35, 26, 26, 1] 116 rigid atoms, others: [25, 20, 21, 22, 23, 24, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 463 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: REAL300025479144 none CN(CC1CCN(C(=O)CC2CC=CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [67, 48, 32, 32, 32, 32, 19, 6, 19, 1, 1, 1, 1, 1, 1, 1, 32, 67, 81, 81, 88, 88, 116, 116, 116, 116, 116, 67, 67, 67, 48, 48, 32, 32, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 88, 88, 116] 116 rigid atoms, others: [45, 43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 44, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 386 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479144 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479144 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479144/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479144 Building REAL300025479145 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479145' /scratch/stefan/7787258/working/building/REAL300025479145 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479145 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479145/0 /scratch/stefan/7787258/working/building/REAL300025479145 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1053 `/scratch/stefan/7787258/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)C2(C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479145 none CN(CC1CCN(C(=O)C2(C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 1, 13, 34, 34, 72, 106, 181, 181, 181, 181, 181, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 72, 72, 181] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 44, 34, 14, 45, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 483 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479145 none CN(CC1CCN(C(=O)C2(C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 80, 108, 155, 181, 181, 181, 181, 201, 201, 201, 201, 201, 201, 181, 36, 80, 13, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 155, 155, 181, 181, 181, 181, 181, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 36, 36, 1] 201 rigid atoms, others: [48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 792 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479145 none CN(CC1CCN(C(=O)C2(C)CCC2)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 18, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 6, 36, 60, 60, 101, 138, 201, 201, 201, 201, 201, 36, 36, 36, 18, 18, 6, 6, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 101, 101, 201] 201 rigid atoms, others: [43, 38, 7, 40, 9, 10, 11, 12, 13, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48]) total number of confs: 588 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479145 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479145 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479145/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479145 Building REAL300025479146 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479146' /scratch/stefan/7787258/working/building/REAL300025479146 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479146 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479146/0 /scratch/stefan/7787258/working/building/REAL300025479146 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1054 `/scratch/stefan/7787258/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479146 none CCC(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 2, 7, 1, 2, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 44, 72, 146, 146, 146, 146, 146, 1, 8, 8, 8, 8, 8, 7, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 44, 44, 146, 1, 1] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 43, 44, 23, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 383 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: REAL300025479146 none CCC(F)C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 201, 146, 173, 146, 146, 146, 132, 101, 63, 101, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 146, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 132, 132, 101, 101, 101, 29, 29, 1, 146, 146] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 822 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479146 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479146 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479146/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479146 Building REAL300025479147 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479147' /scratch/stefan/7787258/working/building/REAL300025479147 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479147 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479147/0 /scratch/stefan/7787258/working/building/REAL300025479147 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1055 `/scratch/stefan/7787258/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)CCCF)C1)C(=O)CSC1=NNC(=O)[N-]1) `REAL300025479147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479147 none CN(CC1CCN(C(=O)CCCF)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 4, 4, 16, 20, 33, 1, 8, 12, 12, 16, 16, 40, 40, 40, 40, 40, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 16, 16, 23, 23, 31, 32, 1, 1, 16, 16, 40] 124 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 13, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479147 none CN(CC1CCN(C(=O)CCCF)C1)C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [33, 32, 33, 35, 40, 40, 40, 40, 50, 50, 114, 124, 124, 40, 27, 32, 13, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 35, 35, 40, 40, 40, 40, 40, 114, 114, 124, 124, 124, 124, 40, 40, 27, 27, 1] 124 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 521 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479147 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479147 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479147/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479147 Building REAL300025479148 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479148' /scratch/stefan/7787258/working/building/REAL300025479148 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479148 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479148/0 /scratch/stefan/7787258/working/building/REAL300025479148 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1056 `/scratch/stefan/7787258/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F) `REAL300025479148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING: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: REAL300025479148 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 1, 1, 5, 13, 13, 30, 30, 58, 82, 144, 144, 144, 144, 144, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 58, 58, 144, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 43, 44, 34, 21, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 390 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479148 none CC(C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 144, 149, 144, 144, 144, 134, 94, 80, 94, 36, 80, 13, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 144, 144, 134, 134, 94, 94, 94, 36, 36, 1, 144, 144] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 914 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479148 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479148 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479148/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479148 Building REAL300025479149 mkdir: created directory `/scratch/stefan/7787258/working/building/REAL300025479149' /scratch/stefan/7787258/working/building/REAL300025479149 /scratch/stefan/7787258/working /scratch/stefan/7787258 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025479149 mkdir: created directory `0' /scratch/stefan/7787258/working/building/REAL300025479149/0 /scratch/stefan/7787258/working/building/REAL300025479149 /scratch/stefan/7787258/working /scratch/stefan/7787258 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7787258/working/3D/1057 `/scratch/stefan/7787258/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1) `REAL300025479149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025479149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7787258/working/building/REAL300025479149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.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: REAL300025479149 none CC1=COC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 30, 40, 40, 55, 55, 81, 117, 201, 201, 201, 201, 201, 10, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 30, 30, 40, 40, 40, 81, 81, 201, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479149 none CC1=COC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 158, 111, 158, 111, 111, 111, 94, 69, 55, 69, 29, 55, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 94, 94, 69, 69, 69, 29, 29, 1, 111, 111] 201 rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 686 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025479149 none CC1=COC=C1C(=O)N1CCC(CN(C)C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 5, 10, 10, 20, 20, 34, 49, 111, 111, 111, 111, 111, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 34, 34, 111, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 44, 25, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 270 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7787258/working/building/REAL300025479149 /scratch/stefan/7787258/working /scratch/stefan/7787258 Finished preparing REAL300025479149 Recording results /scratch/stefan/7787258/working /scratch/stefan/7787258 Appending to /scratch/stefan/7787258/finished/xaaabrt.* 0: /scratch/stefan/7787258/working/building/REAL300025479149/0.* Removing working files in /scratch/stefan/7787258/working/building/REAL300025479149 /scratch/stefan/7787258 Compressing combined databse files /scratch/stefan/7787258/finished/xaaabrt.db2.gz /scratch/stefan/7787258/finished/xaaabrt.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7787258/finished) ======================================================= Finalizing... removed `/scratch/stefan/7787258/working/3D/1058' removed directory: `/scratch/stefan/7787258/working/3D' `/scratch/stefan/7787258/working/protonate' -> `/scratch/stefan/7787258/archive' `/scratch/stefan/7787258/working/input-smiles.ism' -> `/scratch/stefan/7787258/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7787258/working/building' rmdir: removing directory, `/scratch/stefan/7787258/working' ls: No match. ls: No match.